Malcolm in the Middle/WMG

Francis never actually hid "the stash," but instead took it to school with him.

 * Since the boys have literally scoured every inch of the house and probably dug up the entire yard (both looking for the stash and also burying random evidence of their misdeeds, etc), it doesn't make sense that they wouldn't have found the stash by the time the last episode rolls around. They've had something like 10 years to look for it. I think that Francis actually took it to school with him, pawned it there, and used the money to fund his various misadventures there (buying alcohol for parties, things to prank Spangler with, etc. It also explains where he got money to go to Alaska, having never (as far as we know) held a job up to tht point, and obviously not getting the money from Hal and Lois, who don't support his decision. I know that we see him hitch-hiking the last 1000 miles or so, but it is implied that he took a bus at least part of the way there, and he is seen leaving the family's home in a taxi, which he's obviously going to have to pay for.

Lois is really a poor Black Woman
Laugh if you must at this theories title but really think about it, nearly everything Lois says, acts, and thinks throughout the entire series is nearly similar to what nearly every African-American motherly character in the entirety of American television history (From Life With Beula an actual early 1950s Sit Com starring Hattie Mc Daniel to Everybody Hates Chris). She does this so her sons will have a better life and not end up as criminals. However when you really start looking at Lois's behavior and thought process this get a little..wonky.

Lois nearly always complains to other authority figures that her sons are borderline criminals who if they dont act right WILL end up either dead or in prison and after telling the fellow authority figure of some truly bad behavior (that we the audience don't hear) the boys did the figure typically agrees with them (at times depending on the severity of what they did sometimes even her sons (Alternating between Malcolm & Dewey) also agree). However when you look at it the boys aren't really all that bad.

Malcolm is a surprisingly down-to-earth wunderkind that could get any job on earth he wanted, and as it says in other theories below Dewey is such a little charmer he practically bends reality to near his every whim (only doesn't realize it yet). And Reese while has the reputation of The Bad Boy in a seriously more grown up dangerous situation he would probably become useless and not really much of a threat at all. And even their own crazy grandmother believes that Reese by his own thugishness could really make something of himself in a more harsher/stricter society.

All in all in a more realistic sense Lois' constant "worry" is almost literally constant non-satisfaction with her sons and their life choices no matter what they are. Basically the entire Deconstruction of Lois' behavior can be summed up with one..single..point. Their not POOR, or Black or any other minority either for that matter yet Lois constantly acts as if she must save her sons from the Hellhole that is middle class suburbia. Her thought process can be seen as this, since Actual low income single mother/parents push their children as hard as they can in order to "lift" themselves out of their bleak existences and not live the parallel lives of their parents and Lois believes that she is duty bound as a parent to do the same.

So in her mind living in their picket fence quiet neighborhood is no different to her then living in an actual ghetto or slum and if any of her sons have a job that either doesn't (possibly literally) cure all major diseases or somehow dramatically change the world almost overnight they might as well be dropping f-bombs in every sentence and throwing up gang signs. For Lois since they already live a fairly affluent life just fairly successful and/or very rich isn't enough in her eyes her sons must become as close to new Gods/creators of a new golden age for humanity.

This pretty much explains everything from her harsh punishments to her even channeling Chris Rock's mother by figurative proxy ("if you dont do what I say I Gonna slap the (insert name here) out of you"). Oddly enough this also explains why the boys are always meeting Sadistic Teachers and generally mean authority figures Lois probably intentionally places them with these Jerk Asses based on the shows running Aesop of "adversity builds character" (although in Lois' case its probably its more like "Extreme adversity builds Superhuman character".).

Finally in a small bit of Fridge Horror if Lois' sons lived in a filthy stinkin' rich family and were even smarter then they already were maybe she would demand that her sons build something that would make them Literal reality warping gods similar to Dr. Manhattan (Heroes anyone?).
 * So Lois is an Objectivist?
 * You do know that they're lower-middle class and their first son is a criminal, right? And also, that every time she turns her back, the kids are getting into some kind of trouble (including, but not limited to: stealing, sneaking out at night, beating each other up, grifting, skipping school, vandalism, repeated lying, traffic violations, etc.)? Are you watching a different show than the rest of us where the family is normal and not dysfunctional at all, but Lois screams all the time anyway?
 * Part of the genius of the show is that it talks about that particular economic situation, the point in which you are too 'wealthy' for government assistance, or even much pity, but too poor to quite make it without any assistance.
 * Lois understands that they are of a portion of the population that frequently gets neglected by the government. That's why she pushes Malcolm so hard, because as revealed in the last episode
 * Also, Malcolm really isn't a down-to-earth wunderkid, he's shown to be rather full of himself.
 * That's only evident in the later seasons. I think it's a realistic way of showing him getting too preoccupied with his gift over the years since it also happens in real life.

The Virts is designed to discourage the creation of Mary Sues.
You can max out all of a character's stats, sure. But you'll pay for it. The game designers have put in a fiendish feature where a character created to be godlike will instead invariably fail at everything, while all other characters will live wildly successful lives. Take that!
 * Maybe that Malcolm is just really smart, but he has a massive narcissism ego complex and that the Virts was what happens when the virtual world that he creates is actually the real world?
 * There's no doubt that he really is that smart (he beat an entire classroom of geniuses working together to stop him). However, he also made himself incrediably handsome and perfect etc as well.
 * Being similar to The Sims, it makes sense. Although the stats you can edit in Virts may differ from Sims (or some are more importantly monitored by the game than others, like the "handsome/beautiful" scale), the stats being all maxed makes it very easy to work against you if not handled with care. A sim with maxed personality stats (from cheating or otherwise), for instance, could be incredibly energetic, outgoing, playful, clean and nice among other things. But then they are also very sensitive to a point crying fits are common, they get very easily anxious and on-edge if things don't happen (according to them) as they should happen right then and there, they become so playful they take absolutely nothing seriously or become very, very quick to bore or quick to become hungry constantly, they are constantly starving for attention and get so focused on being in the spotlight they can do stupid things from flirt with someone when another person they wooed is in the same room or forget to put on some clothes while running to work when they previously fell asleep naked, and become so concerned everything must be clean to a point they curl up in the fetal position if their house becomes anything less than spotless for too long. It doesn't harm one to have flaws, but having too many flaws overwhelms them to a point they become very unstable because they can't handle too many extremes, unlike a more level-headed, evened-out-personality sim. Malcolm maxes everything out for wish fulfillment (like a mary sue), but then forgets having too much of something without some degree of self-control can backfire horribly.

The Malcolm in the Middle and Scrubs worlds are the same one.
In "Home Alone 4" in season one, they go to a hospital and Laverne is at the front desk. Furthermore, both shows have a serious/funny atmosphere and the worlds seem interchangeable.
 * Furthermore, both shows have the main character providing narration, just in different ways (JD's is internal, and Malcolm is talking to some unseen force). Plus, they never say where either show takes place.
 * Also, Teddy Buckland is there too. Same sad sack as ever!
 * In fact, maybe the reason he seems like such a sad sack in Scrubs is because he's out of his depth. He's a property lawyer when he shows up in Malcolm's world, and that's a whole different kettle of fish to medical law.

Francis is mildly schizophrenic.
Even early in the series, he generally acts like a pretty decent guy who just happens to be a bit of a slacker, especially when it comes to following orders. Usually when he is acting out, he's got a real "crazy conspiracy theorist hobo character" vibe, which provides distinct contrast when compared to his normal self, considering he was originally the most responsible of all four kids and any of the people with which he was associated in their hometown and was the Only Sane Man through a lot of the Alaska episodes. It could fit with the appearance of his actions in the flashbacks to when he was a small child and drove Lois to dumping him with her mom.

This is Malcolm's own personal hell.
At some point in his child life Malcolm did some thing so horrible, that he was sent to his own personal hell, with a she-devil mother, a dad that is being driven to insanity, two brothers that are unreasonable and possibly only there to ruin things for him, and as a whole, a family stupider and more Neanderthal than anyone in the world.
 * He invented the world's first cost-effective Suicide booth! That's why he's constantly being punished for his intelligence!

Dewey's class hamster died of cyanide poisoning.
When he was seen at the end of his arc going up to Alaska, it was when Francis and Piama were driving the other way, the entire area having been declared a Cyanide Containment Area (which makes no sense whatsoever anyway...) At least it's a better end than the starvation he would have ended by if he didn't get run over by a car before the food pellets Dewey left in the ball were all eaten (or suffocation by hamster feces).
 * Your premise is somewhat flawed, it was an arsenic containment basin.
 * That makes much more sense.
 * Proved false as that would be too sad, he found a nice new owner who opened the ball and adopted him.
 * ...What? Did the show become happier while I wasn't watching? And how is it "proved" wrong because it's too sad? Half of the show's humor comes from sadness.
 * You do know that the characters get lucky breaks from time to time, right?
 * I believe the hamster appeared in later episodes as a running gag. With an empty ball.

Lois' obsession with being right stems from her upbringing.
We've seen in other episodes (the one with the burnt dress springs to mind first, but many others exist) where she was completely wrong but refused to accept (in some episodes, even when confronted with proof otherwise, such as the one where the cop stops her for blocking another car) that her first assumption was correct. When she was a child, Ida almost definitely tormented her any time Lois spoke back or even contradicted what her mother said. Lois held it back, convinced that she was right, and never intentionally told a lie to keep from ever being wrong. Eventually, this changed to a believe that she was incapable of being wrong, especially when she got married to a guy who always agreed with her and had four kids that she attempted to rule with absolute authority.

Malcolm and possibly Dewey (but he has fewer problems communicating) have Asperger's syndrome and it comes from Lois' side of the family. Reese and Dewey and Jamie have some sort of hyperactivity.
May sound like something that just popped into a boring fan's mind, but, even though I can't go into detail (it would be too personal...) I'm speaking from experience...
 * Also in the episode where Dewey's friend from the emotionally disturbed class spent the night, Hal said he went and looked for any mistake at all in the dictionary so Reese, Dewey & Jamie might have gotten it from him.
 * Actually, Hal filled in all the holes in the letters of the encyclopedia (colouring in the one hole in the P's, the two holes in the B's, etc.) When Dewey asks him how crazy he really is, he tells him he's on his third set of encyclopedias. It kind of gives you some creepy insight into what Hal's really like on the inside...

Most of Malcolm's family is schizophrenic.
See above for Francis. For Dewey and Reese, they openly admitted to each other that they hear voices when nobody is around. Hal hallucinates all the time - both visual and auditory. Malcolm could go either way - one wonders if the self-narration might be to some entity he's hallucinating - either way he often acts unjustly paranoid. The severity of the symptoms vary (they all confirm to Type I/paranoid schizophrenia, though), but judging from the behavior Hal and Reese have the worst of it, while Malcolm, Dewey, and Francis have more mild symptoms. The latter three seem to have mostly moved into the third phase, while Hal and Reese remain fairly acute.

Reese is gay, though he is not consciously aware of this. What's more, he has an intense unrequited crush on Malcolm.
The argument presented in Pearl Harbor is pretty much spot on. Reese is obsessed with his hair, reads nothing but "men's health magazines", loves to cook, and gleefully watches gay porn when he was able to do so under the pretense of "studying it for Malcolm". He had a girlfriend proximately twice: the first time he ended up trying to nearly kill himself rather than take her to a public dance and the second time he seemed to only be interested in her because Malcolm was.

Reese's one-sided BroYay crush is best highlighted in Malcolm Films Reese, in which Malcolm pretends to get closer to Reese in order to film his antics. Reese basically becomes head over his heels in love with Malcolm (you really only have to see the scene in which Reese whispers into his magic tree that he wants to be together with Malcolm forever), and clearly has his heart broken into itty bitty pieces at the end of the episode. It sheds a lot of light on this rather odd relationship. They start out as normal brothers before puberty, and then Reese keeps on attempting to initiate a Slap Slap Kiss relationship with Malcolm which doesn't fly, because Malcolm is both heterosexual and his brother - so it just ends up slap slap slap. But in the later episodes, Malcolm alienates all his old friends when he gets into high school, so he just ends up letting Reese follow him around like a love sick puppy because nobody else will put up with Malcolm's increasingly bitchy attitude, and Reese keeps on mistaking these signals as romantic, which just makes the whole thing even worse. Tragically screwed up. "Where do babies come from?
 * in the episode where he defects from the military, Reese's Inner Monologue says that he ]love[/dreamy voice]s Green Lantern.
 * And when he needs an excuse to keep Hal occupied:

I thought we'd been over this already...?

Yeah, but I'm blanking. Two guys, right?"

"It's porn, Reese.
 * I do believe they may have been doing this on purpose. * devious grin*
 * Don't forget his solution to the problem in Pearl Harbor was to tackle Malcolm to the ground and roughly make out with him. And that in the series finale, it's highly implied he ended up in a relationship with Craig.
 * He gives him a very visible hickey
 * On the other hand, he did go after the girls in Houseboat, and apparently kept one of their thongs, and in the episode Billboard he did seem to dream about a stripper lady, and also hinted that all women desired was to be strippers. The fact that he'd actually dream about a female stripper would indicate that he at least had heterosexual/straight tendencies.
 * It's called bisexuality. There's no need to dress it up as 'heterosexual tendencies'.
 * Am I the only one who remembers that he was once so upset by a girl breaking up with him that he joined the ARMY? The friggin' army, people! That's love right there. And I'm also disappointed that no one has attempted to make a case for Reese being completely straight. After all, there was an episode that took place after Pearl Harbor that involved the three boys looking at a computer screen. It was a video of a porno with the boys heads pasted on the actual people. The dialogue went something like this.

If it's porn then where are all the chicks? ...Oh."


 * He joined the army after his grilfriend cheated on him... with Malcolm. A case can be made of either being heartbroken for the girl, for Malcolm, or both.
 * More evidence for this theory could be found in the episode when Reese's female friend from the army visits him and he freaks out because he thinks that she has a crush on him.
 * Of course, immediately after he

Lois was physically abusing the boys.
That would explain their absolute fear of her, and why Francis hates them so much.
 * Francis hates her so much because of the psychological abuse and because they're very similar, in that both of them have an overwhelming need to be right, even when they're objectively, certifiably wrong.
 * I can't stand Lois' shouting for a 21-minute episode. Imagine having to live with it. For you entire life.
 * Psychological abuse can be just as bad or worse as physical abuse. Especially if the children really do all have varying degrees of schizophrenia already (see above). Still, Lois only really seemed to have outright abused Francis, due to him being the first child (and thus Lois going overboard from inexperience).
 * Actually, she freaked out, dumped Francis with Ida, and Ida abused him. Shouting, hitting, cutting, enforced cross dressing, I think maybe there was something about cigarette burns in one of the Christmas specials? At least none of that was Played for Laughs.
 * Also, Francis was probably disturbed to begin with. For starters, Francis as a toddler did several terrible things, including dousing his teddy bear with lighter fluid and setting it on fire, and that was before Lois snapped and became a control freak. In fact, it was because of the last action that she even became what she was.

Malcolm is the alternate universe equivalent of Holden Caulfield
An Insufferable Genius with a perception that everyone is a moron and he's the one person on earth with a horrid family and personal problems? Throw in that Francis could be D.B. for being away from home the longest and being a favorite sibling of his, his first person narration in every episode, his girlfriend (the one with the crazy militant father) being alienated by his inability to be mature like Phoebe to Holden and being obsessed with the girl in "Company Picnic" like Holden was to the girl Stradlater went out with at the beginning of the book.

The third option where Hal had to choose to pull the plug or not on the comatose guy was to revive him using virtual reality.
They put a hat on him that included audiovisual output of birds. That woke him up, since you can't hear birds sitting in a hospital room and all he needed was his love of ornithology to intrude on the coma (instead of just his relatives arguing between "leave him on the big, annoying respirator" or "take him off of it and let him suffocate"). Hal never needed to make the decision, since the delay tactic shortly became a solution.

Dewey is Haruhi Suzumiya.
Especially in older episodes, you can see how he can seemingly change reality. You know what? We need to make a page like The Haruhi or something.

Jane Kaczmarek is a VERY bad judge of character.
I mean, for God's sake, she's said in interviews that Lois is a "great mother."
 * Lois is a great mother. Shes definitely a hard ass, but how much more screwed up would those boys be if they didn't have a mother willing to take them on like Lois does?
 * She's a horrible mother. All the screaming and ridiculous levels of punishment, sometimes for no reason, is meant to point out how bad she is as a mother. Notice also that she doesn't seem to get along with anyone else for very long, either.
 * Considering how Francis turned out, with her becoming strict with Francis, it's kind of hard to blame her for being very strict.
 * This is illustrated in one episode where there's a flashback to when Francis was a baby (or a toddler, whatever) and it shows her acting much more timid around her son. In fact, he pretty much walks all over her because she's afraid to punish him for anything. Hal was the one who had to act like a hard ass. Then baby-Francis gets a little too close to danger (I'm pretty sure he wandered near a fireplace) and she snaps. All of her timidness vanishes almost on the spot, and she becomes the bitch we all know and hate/love.
 * Actually, its worse (although you are close on the part relating to fire). He took his teddy bear, doused it with Gasoline, and then attempted to set it on fire.
 * She's a horrible parent, and Hal is a horrible parent for not getting the children away from her. Whether the boys are hellions or not, that doesn't excuse emotional, psychological, and possible physical abuse. Personally, I think the parenting might be the cause of such misbehaviour rather than something Lois needs to 'take on'. If the boys had a loving home, they might have ended up significantly less screwed up. And loving doesn't necessarily preclude strictness. There are ways to firmly enforce boundaries that aren't abusive.
 * She’s not great, but she’s not horrible. Remember, she was raised by an abusive, crazy old bat. It’s only natural that her parenting methods be on the extreme side. As a matter of fact, in comparison with her mother, her parenting is excellent. She goes overboard, yes, but she keeps them fed, bathed, and she gives them a place to sleep. There are even several episodes that show her going far out of her way to make sure that they are well taken care of. That's hardly abusive in my book.
 * Ida did all of those for Lois too. She might not be physically abusive towards the boys(And even that's debatable, considering some of the punishments, like -accidentaly- leaving Dewey a whole night on the corner), but she sure is emotionally and psychologically abusive. And later, financially too.
 * It's a very very sad cycle of horribleness in both parts that Francis started and Lois followed suit with every one of her children. Notably, Francis and Reese have turned out to be better without their influence(Francis took a while, but eventually matured. Reese's only problem was that he had no idea how credit worked, but a talk with Malcolm would have solved that). Also, in one episode Dewey starts behaving good, and Lois follows suit. so it's all really a matter on one part of the "war" changing, and the whole abuse/misbehavior would be ended
 * Lois went from one extreme to the other. Abuse is not something children should ever have to change their behaviour to avoid. Reasonable punishment for misbehaviour and denial of privileges until the bad behaviour is corrected is not abuse. Francis was a toddler with a domineering personality; Lois and Hal's job as parents was to help channel that personality into safe, age-appropriate activities and build a relationship of respect and trust with their son. No, it probably wouldn't have been easy, and yes, they and Francis definitely would have screwed up on occasion. Instead, Lois choose to try to bully Francis and her other children into submission while Hal allowed such abuse to go unchallenged, making him complicit.
 * Francis never actually changed for the better, especially seeing how he still takes joy in getting Lois angry with him, even going so far as to lie about his job status just to hear her reaction. Maybe if Francis was a perfectly normal child before Lois snapped, I could understand why he acted the way he did, but his actions as a toddler indicate that he was long screwed up before Lois took control. A sane child would NEVER try to deliberately douse lighter fluid on something and set it on fire. And to be fair, most of the abuses against his brothers were actually committed by him, not his parents, but him. For one thing, he was the one who locked his brothers up in a closet, stole their toys, tortured them, and scarred Reese with a bayonet. Had that been my kid, I probably would have tried to give him medical help to stop him before he became a danger to society.
 * Yes, they would. Many children of both genders try to set ants on fire with magnifying glasses, they deliberately stomp bugs, they try to create fire by rubbing two sticks/stones together, they deliberately try to cause explosions, etc. Many of them grow up to be sane, productive members of society. Francis deciding to go the gasoline route just proves he was smart enough to understand that gasoline would exacerbate the fire. The parents are still to blame for not stopping his abusive behaviour towards his brothers. And after Francis left, Lois chose to continue to constantly yell, insult, and mete out unreasonable punishments on her children while Hal did nothing to stop her. Whether Francis changed or not is irrelevant. Once he was an adult, Lois could have ceased contact with him but choose to keep trying to get him to conform to her wishes. Although, trying to get Francis medical help most likely would have worked much better than the tactics she chose to employ.
 * Maybe so, but most people who try to douse gasoline on things and set it on fire are usually labelled as insane. There's a reason why people who douse other people with gasoline and then set them on fire are often viewed as crazy. If something like that was considered a sign of inherent insanity, it's very much a sign when doing it in regards to doing it with a teddy bear. And actually, diagnoses for criminal behavior often are tied to harming animals, which Ants/bugs are animals. I agree it was still her fault for not stopping him when he had the chance, but it doesn't make his statements about his actions being from abuse any less false. When I described what he did to my mom, and to my dad, they agreed that he was simply disturbed to begin with.
 * I'm not actually arguing Francis was or wasn't disturbed. I'm pointing out that the statement no sane child would ever attempt such a thing is false. Him trying to do that doesn't prove anything other than the fact he was smart enough to realise gasoline would exacerbate the fire. Whether Francis was disturbed or not, Lois was abusive towards him, and that did contribute to his adult issues. The answer to how to handle a psychologically disturbed child is to try to get them medical help, not to try to bully them in submission. Her other children all have issues and will most likely have those issues for the rest of their lives due to the fact she was abusive and Hal was complicit in their abuse.
 * Okay. Doesn't matter in the end anyways, though. Although I might contribute what I know about this show, regardless of how little, if at all, I've watched it, it doesn't mean I like the show. Actually, the concept of the show (a severely dysfunctional family) is probably something that could be considered a nightmare. Not to imply anything about you guys, though. I only post because, hey, thought I might post some knowledge anyways. It's not really that much different than when kids end up having to go to school despite not liking it one bit to me, really.
 * Justified in-universe: While Lois would be a horrible mother in the real world, her character is exaggerated to compensate for the exaggeratedly rowdy characters of her children. Face it: EVERY CHARACTER ON THE SHOW IS A BAD PERSON! Every character, even if they have good points, does some really nasty and spiteful things because of the Rule of Funny. The arguement made is that Lois's strictness is justified in her particular circumstance, and she wouldn't be nearly as strict or angry with better kids.
 * Jane Kaczmarek isn't a bad judge of character, she's a good actress. Whether or not Lois is a good mother, she clearly *believes* that she is, and it's integral to her character. So Jane Kaczmarek has to try and believe it too.

The boys have most of their issues because of Francis, not Lois.
It's repeatedly shown that Reese, Malcolm and Dewey look up to their big brother, Malcolm calling him his favourite in the pilot. However, Francis has admitted to Dewey that before he left for military school, Francis was a terrible brother to Malcolm and Reese, while Dewey was only spared because of how young he was. Reese, as the second child, mimics Francis' negative qualities by being a bully and not doing well in school. Malcolm on the other hand sees Francis' feud with his parents and mimics the anti-social qualities that he saw at home. Both boys also abuse each other, but they're too close in age to really be able to bully one another so they decide to replicate Francis' mistreatment of them with Dewey. This causes Dewey to retreat into his imagination as a means of escape. Also, he's stifled because of his brothers treating him like a baby, shocked when he shows any sign of having matured.

Francis is a Wizard.
All of the crazy stuff he did to get in trouble as a kid? That was his magic manifesting. But that statute of secrecy is even stronger in the United States, so Francis can't even tell his Muggle family about it. Instead he makes up these ridiculous stories about Military school, Alaska, and a Ranch, and modifies their memories any time they find out anything. Reese has had his memory modified more than the others - he used to be a genius too...
 * Oh my... that makes so much sense.

"Sigh" Okay...
Malcolm will grow a goatee in college and major in robotics, with a side interest in cloning. Increasingly narcissistic and bitter with his family and, eventually, much of humanity, he will eventually leave the United States for Japan. To fit in as much as possible with the somewhat ethnocentric society, he'll change his name to Gendo, mainly because he thinks it sounds cool. While studying for his doctorate, he'll meet one Yui Ikari...
 * Like father(or in this case, mother), like son...

Lois is a good mother compared to her own mother, Ida.
Lois at least is civil with other people and tries to be a good mother. She might get angry easily but who can really blame her, Reese and Francis have done criminal acts before.
 * Lois may be more civil than Ida to others, but she is not civil with others.

Ida on the other hand is rude, selfish and cannot even understand how being nice to other people can make them treat her nicer. When Lois was a teenager Ida made sure Lois suffed her bra. It is very damagaging to tell an alreadly insecure teenager that you chest is too flat and you will never be popular/ a cheerleader if you don't stuff it. Lois even has something of a breakdown when she remembers all the things Ida has said to her that lowered her self-esteem.

Lois has tried to do the exact opposite of what her mother did to her,so instead of ignoring her own children she tries to control them so much that she gets annoyed if anything is wrong.

The sewer entrance in their back yard is a karma embodiment.
Lets just say, both Lois and Hal's kids, and their respective neighbors are the aggravated energies which the whole family ends up feeding. In fact, we all should wonder how or why there hasn't been a pitchfork crowd chasing them down before the series went entirely gone. I like to think that the access to a cesspool behind their home is a cauldron of some sort. The episode with the baby sitter displays what kind of energies everyone feeds to it. Reese mentioned, in exclamation, "I do NOT remember eating this", which either implies that their neighbors excrement exists in this "sewer", or that the waste entered his mouth. The young characters feed to it's vile power in their own special way. Malcom is the pretentious genius with a greedy resolution and ineffective prudence, Reese is the disorganized anti-hero, Dewey is a child with trivial repressions and unhealthy self-esteem. Then there is Jamie, the small child which takes off of Francis (who cannot be included within this guess) mindset. Jamie does not want to cause as much trouble as Francis, but possesses something more dark than Reese. To cap this all off, the Babysitter is the deflection caused by Reese's attempt at fooling their Karma well.

Malcolm is The Doctor and Rees is The Master
Think about Malcolm’s personality of trying to be morally right and superior to everyone else but still being morally ambiguous Rees’s sociopathic personality and how they easily get into fights. Which means that it all started between The Doctor and The Master when one of them took the last blueberry at dinner? This explains Malcolm’s super intelligence as even for someone with an IQ of 165 he still shouldn’t be able to do some of the things he is seen doing (The Master’s just pretending to fool him). This would also explain Lois’s hate as she’s actually The Rani. This would also explain why neither Malcolm’s family has no surname as time lords do not have them.

Malcolm might decide later in life to betray his family, despite giving into their intentions at first.
Well, Francis already did, after leaving the nest and realizing what a mess his life is due to his horrible childhood. Someone did state that Malcolm has come the closest to Francis to realizing what a shit-ass job his family has done raising him, and is even worse off than him.

Herkabe and Lois are brother and sister
In his first appearance, Herkabe’s parents are named John and Ida. It’s established that Viktor and Ida cheated on each other, to the point that Viktor was gone for long stretches at a time. Maybe while Viktor was shacking up with Betty White, Ida was with John. She got pregnant with child and popped out Lionel. Then Viktor called to say he’d be coming back home, so she kicked John out and sent Lionel with him, either because the timelines wouldn’t match up for Viktor to be his dad or because Viktor would expect a son to look more like him than he would a daughter. Lois and Susan were just too young to remember.

This explains why Malcolm and Herkabe have the same Jerkass-Smug Snake personality, explains their similar levels of intelligence and their similar goals (both going to Harvard, and both being interested in computers (though it didn’t work out for Herkabe)).

Malcolm and/or Herkabe may have even realized this at some point, which is why they get increasingly more combative with each other as the series goes on; they’re jealous of the other’s life. To Malcolm, Herkabe is someone who wasn’t screwed up by Ida and became successful in the way Malcolm measures success—being insanely rich, even if he lost it all-- as a result from not being damaged by this kind of upbringing. To Herkabe, Lois was raised in a way that let her have a happy and stable, if dysfunctional, marriage and family while his own marriage ended in a divorce he still seems bitter over, as well as a steady, if low-paying job, while he’s millions of dollars in debt. In the end, his and Malcolm’s fighting isn’t about being better than everyone or petty squabbles over GPA; it’s about being better than ‘’each other’’ to prove themselves and their families; they never let on because they don’t think the other knows, but they just can’t let go.

Malcolm won't become President.
Dewey will, and he'll create programs that help kids of low-income families. Because Lois and Hal's youngest child will be out of the house by the time he becomes President, they'll never see a dime of it.

Cynthia didn't leave for good, she literally disappeared without a trace.
Not in the sense that she was. My theory is that after she lied about having sex with Malcom, the news of the false rumor spreads to Julie's attention. Whom may or may not still hold a grudge against Malcolm from that trash incident. Julie at first believes the rumor considering that kids normally do this. But as the clues begin to debunk it as a fluke, she begins to contemplate revenge against both. This goes horribly wrong when Julie fails to attract the attention of Malcolm while accidentally sending Cynthia away. Right now, the very last area investigators searched in was the local dump. To which is a dead end for the rest of the series.

Malcolm will end up creating The Joker in The Dark Knight Saga.
Or, rather, The Joker will come into being out of various aspects of the Wilkerson brothers' psyches. The brothers tried a magick ritual one Halloween night to play the mother of all pranks on Lois and Hal, and, being the short-sighted idiots they were, accidently pissed off some force on the other side that killed them and used their souls to build a monster. Reese's sadism, Malcolm's intelligence, Francis' determination to rebel, and Dewey's artistic tendencies, all rolled into the most evil motherfucker on God's green earth, determined to do what the boys did best: Upset the natural order and create chaos.

Malcolm was Caroline's lover and the father of her baby.
When you watch how readily she would jump to his aid and would always be much happier once Malcolm was there, it starts to become obvious that there was something more than a normal student-teacher relationship between them. Once the baby was born, she disappeared because they both realized it would be too complicated for her to see the father of her baby every day, all the while knowing they could never be a happy family together.