Final Fantasy IX/WMG

Final Fantasy IX takes place after Dragon Ball GT
There are no more natural saiyans, the genomes were an attempt of creating an indestructible army of clones of one of Goku's ancestors by Garland, but since that ancestor had less than 1/10 of Saiyan blood the clones created didn't have the same abilities as a Saiyan.
 * Gaia is actually the planet where most of the Dragon Ball story unfolds, but it was gradually destroyed after being hit with so many overpower attacks.

Necron is the Iifa Tree
Explained here: http://www.gamefaqs.com/console/psx/file/197338/36121

Necron is the incarnation of Kuja's despair
Just before the final boss battle in Final Fantasy IV, the final Man Behind the Man and ultimate Big Bad, Zemus, is killed in a cutscene by FuSoYa and Golbez while the party watches. Unfortunately, Zemus's hatred was so strong that after Zemus was killed, the hatred itself took on a physical form, the Nigh Invulnerable Zeromus. As Final Fantasy IX is a deliberate Homage to earlier Final Fantasy games, when Kuja dies in the presence of the life-granting Crystal, his despair is so powerful that it, too, is given form, creating a being that exists solely to annihilate the universe because "all things live to perish." Furthermore, Necron's dying words and Zeromus's dying words are very similar: "Zeromus:

I will not...perish...so long as evil...dwells in the hearts...of mankind. G...gh... GRRRAAGH!

Necron:

"This is not the end."

"I am eternal..."

"...as long as there is life and death...""

Necron is the Final Boss of Final Fantasy III
The final boss of Final Fantasy III is the Cloud of Darkness. In Final Fantasy III, if the Balance between Light and Darkness gets messed up, whichever power is stronger will overwhelm the other and destroy the world. During the course of the game, you learn that in the past, the Warriors of Darkness defeated an out-of-control incarnation of the power of Light (which would have burned the world to a crisp). This time, Darkness has become too powerful, and your party, the Warriors of Light, eventually end up having to battle against the Cloud of Darkness, which is going to return the world to nothingness. The literal translation of Necron's Japanese name is "Darkness of Eternity", and it wants to do the same thing as the Cloud of Darkness: turn the world into a state of nothingness. Again, it's one of Final Fantasy IX's many ShoutOuts to earlier games in the series.

Necron is actually Doctor Manhattan.
The resemblence is all there in the boss battle: Necron is (pale) blue, bald, and the humanoid half of his body is certainly muscular enough. So obviously, after leaving Earth, Doctor Manhattan spends many centuries refining his powers before setting forth on his mission to create life: in this respect, he creates life of several formerly barren planets- two of which are Terra and Gaia. He also gives several of his engineered species latent supernatural powers in the form of magic, before retreating to the Crystal World, the replacement for the totalled Glass Palace left back on Mars. However, after watching his creations war and kill over the next several million years, he begins to lose faith in life again. By the time Kujah's Suicidal Cosmic Temper Tantrum comes to a close, Doctor Manhattan is ready to obliterate all his old work in the new galaxy and focus on something different. However, his defeat forces him into yet another epiphany, and he decides to give his creations another chance.
 * And Zidane's speech about not being afraid and wishing to live on (and proving his desire to live by fighting and triumphing), reminded him of his epiphany, years and years and years ago, on Mars about how truly miraculous life is. Also, Necron/Manhattan's proclamation of being eternal was just an echo of his final line in Watchmen: "'In the end'? Nothing ends, Adrian. Nothing ever ends.'"

Necron is Nyx.
After all, at the end of the battle,
 * Does that mean that Kuja's the Nyx Avatar? That makes too much sense. -sighs-

Necron is Death.
As in The Grim Reaper. Anthropomorphic Personification and all that Jazz. The fight against him happens for EVERYBODY when they die, which happens to the heroes after Trance Kuja takes them down with him. The reason it doesn't happen to you earlier in the game is because you couldn't possibly win against him up until the Endgame. The reason he acts like Zeromus is to trick the heroes into wanting to fight him; since they're clearly good people who really don't deserve to die, he decides to not give them a choice as to whether to take the test to come back to life.

Necron is the final boss of Final Fantasy IX.
And nothing more. Square left his real identity ambiguous because we don't need to know it.
 * Now that's just crazy.

Necron is Nekron

 * Not only are the Names the Same, but they have the same motivation and personificational aspects.

Forgoing Necron, Zidane is an alternate universe equivalent to Edward Elric.
C'mon, Chaotic Good mid-teen short blonds with a preference for shorter bladed weapons in non-magic combat and long hair tied back voiced by Romi Paku? Yeah, there's the whole "FFIX is SD" thing, but I've noticed that several characters are taller than Zidane by more than just "He'll grow" standards. (And in Dissidia, Kuja seemed of comparable height to the rest of the characters who aren't wearing horned helmets.)
 * It would technically be more correct to say "Edward is Zidane in an AU", since FFIX was released before FMA began publication (2000 and 2001, respectively), but I may be just nitpicking here. There's actually MUCH more to it than that. Besides the obvious similarities in their appearances and personalities, there are multiple instances where the link can be made: Edward has been called a "monkey" (by Nr. 48, in Laboratory 5) and "thief" (by Mustang when he lends him money), and both have a little brother figure (Vivi and Al), whose relationship with them kind of echoes each other. Their differing behaviors can easily be explained by the setting they live in, the way they were brought up, and what hardships they've gone through: had Zidane been more used to Heroic BSOD-inducing situations, like Edward is, he would've shrugged that whole "I'm actually from Terra" business much more easily (and he still does it rather quickly). Not even in the English version of Dissidia they're immune to the "link": sure, Zidane is not voiced by Vic Mignogna, but rather by Bryce Papenbrook. Now, Bryce has done a character in the .hack//Legend of the Twilight anime, named Shugo, who, in Japanese, was voiced by Junko Minagawa, who is often mistaken for Romi Paku... And guess who she voiced in the radio drama of FMA? ...I'm actually thinking of writing a whole paper on this, because it's just too blatant and I'm that crazy.
 * Point, and he's been called monkey more than then, since I've gone deeper into FMA, he also was called monkey in Rush Valley after getting stolen from by Paninya. I don't know why I never updated with more, deeper, similarities.
 * However, Kuja is known for being tall in the original FFIX, so his being average in height in Dissidia either means that everyone else is fairly tall (which is a fair assumption for the villains) or they undercompensated for the Chibi style of FFIX. Zidane might not be particularly tall in FFIX, but he didn't seem to be child-sized when compared to the few normally sized humans (ie, not Steiner and Amarant) who were shown in cutscenes.

Zidane died when he tried to save Kuja
The lines proceeding the last FMV and the FMV themselves are a delusion of Garnet's. Afterwards, She and Tantalus had tea and a good laugh about it, but she never was the same. Even if I don't want to believe this and sincerely hope it isn't true.

Kuja is a Red Mage.
Kuja can use both White Magic (Holy, Curaga), and Black Magic (Meteor, Flare). Furthermore, his hair is pale like all of the Red Mage NPCs one sees on the streets. Maybe that's why he isn't blond like all of the other Genomes - the process of becoming a Red Mage changes the hair pigmentation. Being a ShoutOut to previous series, all of the party members are based (in combat) on the various classes from the earlier Final Fantasies, so it makes sense to have the villain follow that pattern as well.
 * I always put down Freya as a liar about her class, she may be able to jump, but she has the "Dragon" skills that are kinda-magic (Even if the only ones I ever used were Rei's Wind and Lancet) White hair, Awesome Red hat with decoration...
 * Those aren't decorations. Those are her ears.
 * The bat wing looking things? Yeah no, those are not her ears, they're a part of her hat.
 * Ear covers then since they're in the exact same spot as the ears are on every other burmecian.

Tied into my previous theory in regards to FMA, Terrans aren't orignally from Terra, they're from Amnestris
Father won, The world's doomed, Father adopted the name "Garland", and Zidane was just randomly lucky and got Ed's soul in the process. This was more based on the fact that after one-too-many viewings of "Breaching the South Gate" to figure out the exact musical sting that accompanies the blink-and-you-miss-it cut that makes FFIX page pic, I realized Vivi had a transmutation circle under him. (Okay, they're normal run-of-the-mill Instant Runes, but I still went "Hocrap! Human Transmutation!" when re-watching it) Also, we've got two kinds of Homonculi here, the Genomes and Black Mages. Father managed to improve on the original designs of Homonculi, and thus ended up with one that could do Alchemy, who then stole the plans and mass produced these Alchemist Homonculi. Only risk was the shortened life, even without a soul. And now I'm not certain I want Zidane to go back to Gaia afterwards in that fanfic I'm writing...

Qus are actually Eloquent In Their Native Tongue.
They're not simple-minded so much as speaking a second language that they don't bother to learn. This troper suspects they use a Southeastern Asian language, in order to explain the barrel marked with the character for "alcohol" in the feast hallucination had by Quina.

Amarant is Eiko's father.
Because the two are already expies of Shadow and Relm in every other way.

The party came closer to beating Beatrice than she let on.
The way she keeps Stock Break in reserve, and the fact that when you get her its a very high MP cost attack, indicates that she was using it as a last resort. The party might have literally had her on her last legs before she swatted them. She's not almighty when you get her as a party member, and the fact that she gets stronger as the battles go on indicates she may have been doing a bit of Level Grinding herself. Her sparing the rest of the party may be as much respect for how much fight her opponents put up as contempt for said opponents.
 * Makes sense, though she had no need to level grind seeing as she spent quite a while slaughtering her way through a few civilizations before she switches sides, XP gain just makessense.
 * Doesn't really make sense since she strikes you with it after a while, even if you don't attack her at all. She toys with the player party for a while, and then shows her might.

Baku is a legendary hero from Lindbulm's past
Baku is close enough to Cid to be the first person he turns to when he needs Princess Garnet kidnapped, despite seeming to be just the leader of Tantalus. Regent Cid evidently trusts Baku enough to have him flying the Hilda Garde 3 at the end, with the rest of Tantalus on board, despite him owning a large army with other airship pilots. There's also a statue near the entrance to Lindbulm which Zidane says "looks a little like Baku," and it's revealed towards the end that "Baku always loved a grand charge." Plus, he's allowed access to Lindbulm and Alexandria castle seemingly at will, and knows the way around both.

Garland created Jenova
He said that Terra had absorbed many planets before in an attempt to survive, but first they needed to be weakened. So what's to say he didn't construct an animal variation on the Iifa tree and send it to Cloud's world to consume the lifestream and then replace it with Terra's

Zidane and Makoto (and the other Genomes(except Kuja)) are immortal.
Or at least unaging once at the adult stage,since Genomes were intended to receive the souls of the Terrans, who unlocked the secret of immortality,and whose whole plan is too live forever.

The Terrans had 2 different plans for dealing with Gaia.
Plan 1 was Terraforming, which is what turned the waterworld Gaia into a world with livable landmasses. On a related note, all Gaian land life is the result of this process, thus explaining the similarities between summoners,humans, and genomes - including the ability of a single drug to affect all of them roughly the same way. Plan 2 was the thing with the cycling of souls and such, which was turned to when the constructed ecosystem began to behave in unexpected (and to the Terrans detrimental) ways.
 * Nah, the Terrans wanted to merge with planets that had "pure crystals," which I assume means no life (as the crystals govern souls). They didn't want life to develop there. If Terra had been eying Gaia since before there was even any land on it, they'd have had plenty of time to fuse the planets before entire civilizations were developed on Gaia. Granted, maybe their sense of time is a bit off considering how long they "live," but I wouldn't think Garland would go thousands or millions of years before noticing, "Oops, Gaia has people now. When did that happen?" Rather, what probably happened was Terra stumbled upon Gaia long after life had developed and it was just their only option. As for why the Genomes are so much like humans... I'd say that these specific Genomes were designed by Garland to mimic humans after observing life on Gaia, and that Terrans actually used to have some other form. Only problem with that is the giant stone faces in Oeilvert look human.... Summoners, presumably, just branched off a little from humans some centuries back.

Genomes are hardwired to be unable to kill each other.
This explains why Kuja doesn't kill Zidane despite numerous opportunities to do so,even after Zidane becomes an actual problem for his plans.
 * Alternately, Kuja still harbored some kind of lingering fellow feeling or fondness for the younger Genome, despite hiding it really, really well. This actually makes Zidane choosing to go back for him twice as touching.

Garland was Lord Avon.
Reasoning:The play "I want to be your canary" contains a minor character named Zidane. Main PC Zidane is named Zidane. Unlikely coincidence...unless they were both named by the same person:Garland.
 * Don't the rest of the Tantalus (sans Ruby, who isn't an orphan) also share names with the characters? Baku probably named them; Marcus, who seems the oldest, even has the name of the main character of the play. Garland calls Zidane by that name as a Sure Why Not moment.

Final Fantasy IX takes place in the same world as Final Fantasy I.
Garland was named after... Garland, since the king remembered the days when Garland was a knight of Cornela/Corneria. The Garland we see is simply Garland *insert Roman numeral here*. Also, Mount Gulug.
 * Why would Mount Gulug be on a different planet than Garland's homeworld?
 * Presumably, its really New Gulug, named after the original Mount Gulug during that time back in the depths of history when Garland had Terra invade Gaia conventionally. Presumably the name stuck after the Terrans retreated, but the Gaians dropped the "New" part of the name because they didn't know about the original.
 * Actually, if you look at the world maps of both versions, they're quite similar. (The former is FFI, the latter is FFIX.)
 * Aside from the fact that the land tends to be concentrated in the four corners of the map, those maps aren't similar at all.

Adelbert Steiner is an Expy of Patrick Warburton.
If this game had voice acting(or if he appears in the next Dissidia Final Fantasy) it's pretty obvious who'll be voicing him in the English version.

Kuja is an alternative universe version of Franky from One Piece
Both are human, yet not human, and both wear a speedo/thong. Difference is Franky is good and the epitome of manliness, Kuja is VERY effeminate and evil.

Concerning Vivi's children..
Vivi and the rest of the black mages somehow found a way to create other black mages that wouldn't have such a restricted lifespan. They could have worked with the Genomes to find the right way to go about it. So Vivi's children aren't strictly his, but they are black mages created by his idea to give black mages a longer lifespan. So they're more the children of his idea.

Terra is what happens when the Light Warriors lose their first fight with Garland.
In theory, that is an alternate way to break the FF 1 time loop. It removes the need to send Garland back in time, and the Four Fiends' origin. But because evil won in the end, the world turns out darkly. The Lufenish retain their supertechnology, but the crystals are still drained for reasons no one is capable of seeing.

The desparate Lufenish develop dimensional travel and soul manipulation, and eventually put together the Terran's plans as seen in Final Fantasy 9.

For added drama, let's say that the five warriors were caught in limbo when the time loop ended, locked outside of the reincarnation cycle, until the Terrans rescued them. Garland is Garland's reincarnation, and his three angels of death are three of the four Light Warriors (Most likely Black/Red Mage, Thief, and White Mage).

In a related note:

There was a Zeroth Angel of Death used during Garland's first assault on Gaia.
I'm guessing Zero was a Warrior in contrast with the more magic-based reapers developed later.

Cid and/or Hilda are sterile.
Think about it. They both look quite old and have ruled Lindblum for a while, but they have no heir. That would also explain why they adopt Eiko and raise her as their own.