Black Swan/WMG

Nina hallucinated Lily and her sex scene
The girl had just taken ectasy, for one thing, and on top of all of Nina's issues and worries, drugs are never a good recipe for seeing things clearly. Also, after Nina "came to" and ran out of the club, it probably wouldn't be logical that Lily would be able to find her so quickly.

When Nina returns home, Erica never addresses Lily and says nothing like "get the hell out of my house".

There's a nifty camera trick with a mirror that seems to merge the image of Nina and Lily together, shortly after Nina's mother confronts her after they enter the apartment. This is the hint to us that they are the same.
 * This appears to be the most straightforward interpretation of the scene, considering that Nina's hallucinations are moving into full swing by this part of the film. Also, when Lily denies that she stayed the night, Nina seems more embarrassed at having had a sexual dream about Lily than confused and angry at Lily for lying.
 * Considering how sexually repressed Nina is, how her first masturbation scene went, and how Lily embodies the darker, edgier, and seductive Black Swan that Nina so desperately wants to become, it's extremely likely that Lily was telling the truth and Nina hallucinated the sex scene. Particularly since Nina's mother never acknowledges that another person is in the apartment.

The sex scene with Lily was real
We do see it happen.

WMG because Lily specifically denies it.
 * Lily could have denied it because she was simply a closet case.

It was All Just A Hallucination
None of the events of the movie happened. Nina never got the part for Swan Lake, which caused her to completely snap and hallucinate a world where she did get a part; but because she's crazy the hallucination is odd.

Thomas Leroy was an officier in the French Foreign Legion
More people have died during the Legion's training process then any other military unit in the world. He applied the same ideals on the ballerinas that he trained.

It was All Just A Hallucination except for the very end
In reality, Nina had a perfect life. She dances the black swan just fine, she has a great relationship with her mother, all the other dancers adore her, Beth fully approves of her taking over her position, and she has a fine boyfriend off in the background somewhere. And she totally ate that cake. Opening day comes, she's getting all ready to debut as the black swan, and then...freak accident! She fatally injures herself in the dressing room. Fueled by the adrenaline rush, she proceeds to dance the rest of the ballet perfectly, but as she lies dying she can't cope with the fact that in the midst of all this perfection, one little accident has brought her career (not to mention her life) to a premature end. So she invents a new history for herself, in which her life isn't perfect - in fact, it's downright horrifying - but that single slip-up, the accidental stabbing of herself, she now envisions as a controlled and even empowering action that enables her to dance a perfect black swan. One little screwup mars her otherwise perfect life, so she hallucinates a reality in which it improves it instead, by her own twisted ballet-dancer logic.

Black Swan takes place in the same universe as Requiem for A Dream
And of all Nina's delusions are her bad reactions to drugs, first diet pills, then ectasy. Even in scenes when she doesn't seem to be on anything her mind is still messed up and she hallucinates.

Which would mean that this movie has the same Aesop as RFAD: Don't do drugs!
 * This could also be supported by the appearance of Uncle Hank (A.K.A the ASS TO ASS! guy from Requiem) making creepy kissy faces at Nina in the subway.

Beth was only real during the cocktail party
From all the scenes in which we see Beth, the only one with the real Beth is the cocktail party where they announce her retirement and Nina's becoming the new prima. All the other scenes, Beth freaking out, Beth begging Thomas to take her back into the company (after the cocktail party), Nina going to the hospital and seeing Beth's injured legs, and of course Beth stabbing herself in the face, are all things Nina hallucinated because of her own fears (influenced by her mother's career) about getting old and unable to dance anymore. The things Nina takes to the hospital and Beth claims she had stolen from her were always Nina's, she is seen placing them on her dressing table after she is told she would be sharing the dressing room with Beth, but is not seen previously taking them from Nina's belongings. So, there weren't only White Swan!Nina and Black Swan!Nina, but also Beth!Nina.
 * Well I forgot about the other things, but she did steal the lipstick.

It's a story about rape and an abusive relationship
Thomas is obsessed with Nina and ended up raping her before the movie. Nina suppressed her memories of that event, but the trauma manifested in her hallucinations about becoming a swan. During the movie, Thomas manipulates her -because he knows she is emotionally unstable- by casting her as the main character but telling her he hadn't, pushing her physically more and more, emotionally attacking her with aggressive and dismissive remarks about her sexuality -also a manifestation of his own frustrated lust for her-, and molesting her after having made her vulnerable with said remarks, all in order to break her and eventually drive her to suicide.

Nina's mother Erica is also a hallucination in the film. (Or mostly a hallucination) Nina lives by herself.
I just saw the movie once, so I'm not sure if there's much evidence for this. Erica doesn't interact with anybody but Nina, doesn't ever leave her apartment except for a short shot of her in the audience. Nina isn't ever let in, she always unlocks the door herself. Her scene shooing Lily out of the apartment could be interpreted as Nina answering the door twice to a *real* Lily, or all Nina. She never wakes Nina when she oversleeps, and she's wearing the same thing in every scene she's in. After Nina and Lily's "sex" scene, I think I remember her waking up in her own bed. The only thing I can't account for is calling in sick to the performance.

Le Roy is either asexual or gay.
He only invokes Casting Couch in order to get his stars to perform to the best of their abilities. And it works.

The movie is a criticism on how the ballet industry treats its dancers.
Ballet is full of harsh and often unrealistic body expectations. Dancers often work themselves to exhaustion or worse, the life expectancy for even the best of careers is often terribly short, eating disorders are all but (explicitly) encouraged, and minorities are pretty much non-existent in the big name companies. The director saw all this happening and decided to make a commentary on it... and it's not exactly flattering.
 * Alternately...

The movie is a criticism of 'method acting' and the idea of 'becoming' roles in general.
The whole movie is about Nina going completely loco from trying to 'become' her character. Her whole quest to become the Black Swan pretty much breaks her emotionally. I think the director is giving us a little cautionary tale about overdoing it.
 * This makes a lot of sense when you realize that both Nina and the Swan Queen commit suicide at the end of the performance, the Swan Queen because she's so traumatized and Nina because it's the only way for her to be "perfect".

Nina never actually broke her Stage Mom's hand
It was a metaphor for her finally breaking free from her grip. This is why Erica is seen at the performance, seemingly unharmed.

Nina never actually died in the last scene
How could no one notice all the blood on her white costume? How come Lily was the only one who noticed something was wrong when she was obviously covered in blood? It seems far more likely she just slipped into some sort of coma as she fell, which would explain why Tomas was yelling for someone to call an ambulance. Any talking she did was simply a hallucination, much like the mirror shard in her stomach.
 * Or perhaps she DID stab herself, but it wasn't nearly as bad as she imagined it to be. After all, the blood didn't actually start to spread dramatically until she was up on the cliff as Odette, about to die. It could have been an exaggeration in her mind of how bad her injury really was.
 * Or the glass was acting the a pressure barrier limiting the bleeding. Like how in the event of an actual stabbing your not supposed to remove the blade?
 * That's true, she did manage to dance the entire second act of Swan Lake without passing out or dying. Plus the glass didn't look like it was that far in.
 * There's also the fact that she has to change into her Black Swan costume after the initial stabbing, and then change back into her White Swan costume. The hole that she takes the mirror shard out of is just too perfectly over the wound to be real, I think.

Black Swan actually takes place in the universe as Inception - and Paprika
In fact, it's the story of an attempted inception. When dream entering technology first appeared started, it was a very risky, tenuous business. The only way scientists could explore dreams was to create new personas for themselves - Sugar and Ice Personality Dr. Chiba became Paprika, to start. This is the story of an American scientist, Nina, trying to build her dream persona - and she manifests as a ballet dancer, because she loves ballet, and always wanted to dance ballet as a child, but she's a stiff, methodical, regulated one, because she's become used to living a methodical scientist's life. But to Thomas (a more experienced dream enterer, a scientist who dreams he's a Frenchman for reasons yet undisclosed to the general public), that's not enough. Nina's got to fully connect with her Id for her to be successful, in his view. So it's a shared dream between the two of them - with possibly a couple of other people, but the point is, everyone in the film who's trying to hurt Nina actually is, because they're Projections of Thomas' subconscious. Problem is, Thomas has gotten too much in touch with his own Id. As he's in control of the dream, he also is lusting after Nina, and Nina is having difficulty handling her own sexual desires/problems. As the dream progresses and gets out of hand, Nina is forced to confront her own childhood traumas and sexual repression, and finally - in an inadvertent gesture that only makes sense to Oscar Wilde - she finds a way to die in the dream. She dances a perfect, amazing Black Swan, and then dies, waking up, leaving Thomas and his sick world behind.

There's a Malkavian on set after Nina's part
The Malkavian was part of the ensemble and really wanted Nina's part, so started throwing down some heavy Dementation on her. This backfired spectacularly, as it only made Nina more determined to play the Black Swan. Come to think of it, do we ever see Lily in direct sunlight?

Nina killed Beth
After the scene is over, you see her holding on to a bloody file. She couldn't deal with the idea that her idol wasn't perfect, so she snapped.

The entire story is taking place in Beth's mind.
Beth was a famous ballerina who got into a car accident and received a permanent injury on her leg. Her career is ruined and she has noone to blame but herself, so she invented the story of a girl named Nina Sayers who honed in on her territory so she'd have someone to be mad at. Nina never existed.

Lily has been gaslighting Nina from the start.
Before Lily made the trek from San Francisco to New York, she did some research on the other soloists (easy enough in this day and age) to see who is her biggest competition. She knew that Nina was probably it, and upon arriving, discovered that she was going to be easier to break than she thought. Lily interrupted Nina's audition on purpose, was the one who wrote "Whore" on the bathroom wall, and was lying about not spending the night with Nina, etc. None of this was to drive Nina to suicide or anything, but it was simply to get her stressed out enough to make major mistakes, miss performances, etc. Listen to how Lily cries out "She was supposed to be sick!" when Nina shows up at the performance after all. Things did not go according to plan. However, Lily is genuine when she offers her congratulations during the performance, and when she sees Nina's injuries at the end, she is horrified that her ruse went so far.
 * That wasn't Lily. That was Veronica, who was the girl Nina originally congratulated for winning the part. She was likely Nina's lead understudy and her true rival for the part.
 * You mean it wasn't Lily who cried out "She was supposed to be sick!"? Yes, it was - Lily was made Nina's alternate.

Lily: the wild child but completely innocent bystander
Besides offering her Ecstasy in the nightclub, what did Lily actually do to her? She's very well meaning nice and even sticks up for Nina when she notes her distress. I think she feels really bad for her and sees how repressed she is and offers up her friendship because of these reasons.
 * That's what I thought as well. Also, it looked to me like most of Lily's crazy/nasty/psycho moments were Nina's paranoia; I didn't think she was at any point trying to steal the role.

Lily has gone through the same mental breakdown as Nina
Every time she tries to get Nina to stop performing, she's really doing it to save her from the brink of insanity. However, when she had her breakdown she never had anybody protecting her, and didn't realize that Nina's going even more insane. When she freaks out at her being sick, she isn't mad but scared for her. and when Lily congratulates Nina in the dressing room, she thinks that Nina may have finally gotten a hold of herself.

Thomas deliberately injured Beth, or at least instigated her suicide attempt.
Beth and Thomas obviously had a very intimate relationship, possibly very crucial to her getting the role of lead dancer. Thomas kicking her out of the company would be her opportune moment to bring forth sexual harrassment charges against him. Luckily for him, she winds up in the hospital, badly injured, mentally unsound, and potentially suicidal. If she tried to press charges now, who would believe her?

Nina is Madotsuki.
Closely related to one of the above theories. Also, if we believe some of the hypotheses in the Yume Nikki wild mass guessing page,.

Nina really did turn into a swan
Note the shadow near the end.

Nina wrote the word "Whore" on the bathroom mirror with Beth's lipstick
She spends the majority movie battling herself. So it makes sense. Also, we never actually hear anyone else come into the bathroom, and it happened too quickly for them to have done it without her noticing.
 * This one's too good not to be intentional. Nina steals the red lipstick from Beth only a few scenes before, and then we see her decide to wear it when she goes to ask Thomas for the part. Thomas kisses her, she gets the part, and she feels like a whore. Later, she enters the bathroom alone so she can call her mother, and perhaps sees the lipstick in her handbag when reaching for her phone. She's reminded that she'd wore it with the intent of influencing Thomas, and labels her reflection accordingly.
 * Interestingly, as seen in the "Making Of", Darren Aronofsky had Natalie Portman herself write the word "Whore" with the lipstick, rather than just have a set dresser or crew member do it.

The film is meta
During his first speech, Thomas Leroy says that he wants to do a revolutionnary modern version of the Swan Lake, and I think the film actually is that version. The film begins with the beginning of the ballet (in Nina's dream, as she tells her mom when she wakes up), and ends with the swan's suicide. I think it could be split into three acts, but I would have to watch it a second time to determine. The movie tells the story of a young girl, in a body she doesn't like and doesn't even own (Nina of course, trapped at home, on diet, cutting herself, hurting her feet...), following a curse by a wizard (Erica, always dressed in black, and the origin of all of Nina's issues).

The girl then meets a prince (or a king, or even Leroy !), who is seduced by the white swan, but ends with the eponymous black swan, while the girl kills herself.

Here one of the creative touch of the movie is on the casting of the black swan. In the beginning all leads to think it's Lily (Nina's darker twin in many ways, and she even sleeps with the prince... maybe), but it seems to actually be Dark!Nina herself, who takes a kiss from Thomas in the end.

I wish a troper could find a place for Beth in that theory, though. Also, it prevents me from being bugged by the fact that Leroy's take on the Swan Lake is not that much original...

Thomas is actually a pretty awful director.
This solves an amazing number of gripes within the film, I've found.
 * What are those? I feel like having a pretty generic version of Swan Lake is one of those.

The Movie is a Super Villain Origin Story
Nina slowly goes insane, and develops at least some psychotic tendencies- plus how awesome a villian name would "the Black Swan" be? She may or may not have swan related Voluntary Shapeshifting powers.

The movie is a deconstruction of the White Swan Ballet itself
Okay this may be stretching it a bit but think about it, the movie lays it all in front of us, the white swan and black swan are played by the same ballerina, but the white swan is supposed to be pure while the black swan is nothing like the white swan. This comes up several time throughout the movie and Nina at the end of the movie kills herself. The white swan and black swan are different personalities who can't coexist within the same body and thus a conflict who is in control takes place. Should she stay the black swan or the white swan, the white swan hates the black swan because she steals everything away from her, so Nina responds by killing her, thus killing herself, like the white swan in the original ballet.

Lily doesn't actually exist
She's just Nina's id. Hell, why not?
 * Then why is Thomas having sex with her?
 * Wasn't Lily having sex with one of the dancers in the troupe and Nina simply imagined it to be Thomas? This troper thought the scene where she sees Lily caressing the dancer later during the show is where Nina realizes that she hallucinated it to be Thomas. It's just before she realizes that she hallucinated the entire fight with Lily in the dressing room and actually stabbed herself, if this troper's not mistaken.
 * It may work on a similar principle to ?
 * Nina just imagined it? Hell, with all the Mind Screw in the film...
 * Also, I don't know if I believe Lily doesn't exist, but it's entirely possible.
 * Maybe he was actually having sex with Nina.
 * There are plenty of clues that point to this idea, including, but not limited to the following:
 * 1) Lily is first introduced when Nina is first asked to dance the black swan (during her audition).
 * 2) Despite his interest in doing a radically different version of Swan Lake and his conviction that Nina and Lily perfectly embody the Odette and Odille respectiely, the director never considers splitting the role in two, which is commonly done.
 * 3) When Lily just randomly shows up at Nina's apartment, Nina doesn't know how Lily knew where she lived, and Lily's coy about it.
 * 4) When Lily comes to the door, Erica insists that "it's nobody"; when they seem to return together, we only see Lily in reflection shots; Erica and Lily never interact.
 * 5) Nina taunts her mother with the idea that she slept with two men at the club (Tom and "Jerry") -- but we only see Nina with one guy and are later told that Lily went home with the other.
 * 6) Lily is seemingly never reprimanded for anything, including arriving late, disrupting a rehearsal, and refusing warm-up exercises. When Lily startles Nina causing her to stumble during her audition, the director blames only Nina and refuses to let her start again. Further, when Lily tells the director to go easy on Nina, he gets angry at Nina, as though Nina had asked him this.
 * 7) Lily's tattoo is somewhat improbable for a soloist in the New York City Ballet.
 * 8) Lily's interest in Nina is one sided and out of nowhere; we never see a real friendship between them, only Lily showing up and dragging Nina into various questionable activites.
 * 9) Like Erica, the director also refers to Lily as "nobody" at one point in the film ("nobody's trying to steal your role").
 * 10) The director's obsessive interest in bringing out the black swan in Nina would make more sense if he'd actually seen some Black Swan potential in Nina's dancing; if Lily's actions are actually Nina's, then it would imply Nina's Black Swan is frustratingly inconsistant, not flat out hopeless.
 * 11) When Nina arrives late and Lily appears to be filling in for her, Thomas makes no attempt to verbally acknowledge that this is going on, and when Nina does, he looks completely confused as to what she's talking about.

Nina is reborn in the end of the movie
According to Natalie Portman, Darren Aronofsky chose the placement of the blood on Nina's dress to make it resemble menstruation, so that it would symbolize Nina becoming a woman. As someone noted above, it seems unrealistic Nina could've danced the whole second and third act (if we accept that Nina stabbed herself at the exact moment when she imagined stabbing Lily) without anyone noticing the bleeding. Also, it seems too convenient that the wound only starts bleeding heavily when the White Swan dies. Therefore, the wound either doesn't exist or is much smaller than what Nina thought. (Just like she imagined tearing the skin off her finger and causing a big wound, when in reality it was just bleeding a little.) So Nina doesn't die in the end.

Nina is at constant conflict with her superego, who says she should always remain in control, and her id, who says she should give in to her carnal desires. The superego in the movie is her mom, and the id is Lily. Nina is afraid that Lily, who is more in touch with her base instincts, is better at the role of the Black Swan, which is all about the id. That's why she externalizes her own id to Lily, imagining having sex with her, and fears Lily is trying to steal the role of the Black Swan from her. The mother, on the other hand, is constantly trying to control Nina, and in the end she even tries to stop her playing the Swan Princess, because she thinks Nina is losing her mind due to her role. The mother, therefore, is the superego, always keeping Nina in control and not letting her lose herself to her instincts. Because Nina has externalized both her superego and her id, she cannot grow up. She remains a little girl who can't take control of her own life or become a sexual being; that is, she cannot become an adult woman.

In order to grow up Nina needs to accept her superego and id as internal to her, and symbolically "kill" their external representations. She first does this to the mother, attacking her and saying she is moving out. (Significantly, she attacks her hands. The mother in the movie is sort of a puppetmaster, and she uses her hands to paint pictures of Nina, thus recreating Nina in the way she wants her to be. Breaking the mother's fingers is a symbolic attack against her control.) Then she does it to Lily, stabbing her. Only after she has done these things can she fully become the Swan Princess. It's important to notice that after Nina has stopped externalizing parts of her own psyche to other people, the mother and Lily are no longer her "enemies". Lily comes to Nina's room to praise her performance as the Black Swan (the role Nina feared she would steal from her), and her mother is seen in the audience, looking ecstatically at Nina's performance of the role she previously feared would consume her daughter. This means Nina's superego and id have become part of her, and they're not represented by other people anymore. She has finally become a grown-up woman, and this is symbolized by the blood on her dress, resembling menstrual blood. Nina doesn't die in the end of the movie, but is reborn as a mature human being, as someone who can reconciliate her need for control and desire to let it go.

A female Bildungsroman
Everything happens more or less as the movie shows from Nina perspective. The weird things are hallucinations, triggered by extasis, sleep deprivation and stress. The movie shows how Nina grow ups. At the start, Nina is a insecure ballet dancer, with mommy issues, a childish and insecure young woman. The movie shows how she externalize their fears and hopes relating to be an adult, in a alucinatory doppelganger, and later project it into a Lilly. Finally, after the murder hallucination, Nina embraces her "dark side" (or, maybe, a sexual unrepressed identity) and come into adulthood, or perfection, integrating both sides in herself. At the end of the movie, she simply faints due exhaustion, and the blood are another hallucination meaning their nirvana like deathwish.

The blood at the end is Nina's mind telling her she's having a heart attack.
Nobody reacts to the blood until she's lying on the mattress, suggesting it was all in her mind, however, she doesn't look well. It also makes sense given she looks like she hasn't had a good meal in a long time.

Erica is actually a perfectly good and loving mother
Nina is bulimic, compulsively picks at her skin, and hallucinates from early on in the film. Her mother may be overwhelmed, frustrated, and scared at what is happening with her daughter, but she isn't unhealthily controlling; she's taking care of her mentally ill daughter to the best of her ability. Nina's bedroom door doesn't have a lock because Nina is prone to self harm. Her mother clips her nails because people who compulsively pick sometimes seriously injure themselves (alluded to in some of Nina's more gory hallucinations). Rather than pushing her daughter to go for the biggest roles in typical Stage Mom style, Erica actually tries to talk her daughter out of competing for the Swan Queen, concerned about the amount of stress the role will put on her unstable daughter -- rightfully, as it turns out. She's only overbearing from Nina's point of view, and that's because Nina believes she can take care of herself when in reality, she requires a guardian.

Beth has been through the same mental breakdown as Nina.
Beth seems a little...Insane, just like how Nina was turning out at the end. She also  Thomas also says her self-destructive tendencies made her compelling, and Nina is implied to have an eating disorder and impulsively scratch at herself. Beth is what Nina will become when she gets older: bitter, clingy, still mentally imbalanced.

Nina had sex with Thomas, not Lily.
Given how frequently Nina and Lily seem to merge, it is possible that Nina actually had sex with Thomas, but ended up being so disgusted or frightened by it that she imagined it was Lily.
 * Or alternatively, Nina was actually having sex with Tom from the club, (who could in fact be Thomas, after all, Tom is short for Thomas.)

The entire movie happened, as shown.
Nina is a mentally unstable Reality Warper who had her powers bound and her memories erased for the protection of herself and those around her. Her "mother" is a guardian appointed by the others of her kind to keep her from remembering. However, she failed and Nina's original, destructive personality and powers re-emerged. None of the movie shows "hallucinations" or "visual metaphors" are those, they're all literal.

The enrite movie takes place in The Matrix.
Nina got out of the Matrix just not with her sanity.

Nina is falling to The Dark Side.
She is a distant descendant of Padmé and Anakin in our galaxy.

Nina is a teenaged girl, and she is being sexually abused by Thomas and her mother.
The world of professional ballet looks nothing like what we see in the movie because it isn't one: it's a ballet school, Thomas is an instructor, and the Swan Queen production is a one-night performance by students. That's why she has a little girl's room, that's why she's only now discovering her sexuality, that's why she's able to land the top spot in a highly competitive ballet despite being timid and meek, that's why her mother coddles her like a child, and that's why she's expected to dance both roles without that being considered overly taxing or potentially harmful: she's probably only fourteen or fifteen years old. Nina imagines her ballet school as a professional company because it is the only thing her mother allows her to do with her life; she doesn't go to school or have friends, and her relationship with Lily is perfectly normal (if extreme) teenaged rebellion.

Erica is emotionally abusive and manipulative, but she goes to specific pains to control Nina's body: she forcibly clips her fingernails with scissors, scolds her about having perfect skin, uses emotional blackmail to control her diet, constantly invades her privacy, and paints obsessive pictures of her. In the cake scene, Erica goes to throw it out until Nina apologizes, and then only offers her a bit of icing by letting Nina lick it from her finger, almost as an act of supplication. Nina's psyche is already crumbling (the eating disorder, the cutting, and so on) as of the start of the movie because of the years of sexual abuse, which leads her to seek refuge in the only place her mother gives her to be away from her: ballet. She studies ballet under Thomas, who we see in the movie sexually assaults her at least twice.

The reason her mind splits into Odette/Odile is the violation of both herself and what she thought was her pure space, and she's warring with the guilt and shame of being sexually abused, but remaining silent in order to keep her role and the peace in her home, against the pure, untouched perfection she wants to recapture through performing.

Lily and Nina really made love; the scene where Lily denied it was Nina's hallucination.
Lily is in love with Nina and really just wants what's best for her, and is doing her best to be a good girlfriend to someone who, unbeknownst to her, is deeply mentally unstable. Nina, in her madness, hallucinated the scene where Lily denied sleeping with her, as well as all the other scenes where Lily was trying to sabotage or undermine her. Nina has a very low sense of self-worth, and cannot bring herself to believe that she is worthy of being loved, so she imagines that the woman who loves her and just wants to be with her and make her happy is really her enemy.

Nina's mother doesn't exist
Honestly, look at how she appears in the film and throughout. She's constantly in Nina's face, almost like a Fight Club type of deal. She actually died recently and all of it is actually her influence still in Nina's subconscious.

Nina's Mother was molesting her
The scene with Nina in bed and her mom entering the room in a bathrobe, saying "are you ready". Also, the sex scene between Nina and Lily actually happened between Nina and her mom. Remember Lily saying "sweet girl" near the end of it.

Thomas intentionally instigates the destruction of his lead dancers.
We don't get to see Beth's attempted suicide, and we only hear about it from Thomas. It's worth noting that she threatened to come over to his apartment on the night she was hurt. It's possible that he hurt her himself, or intentionally prompted her suicide attempt.

With Nina, he saw a girl who was easy to take advantage of, but not experienced nor enthusiastic sexually. In giving her the dual role of the swans, Thomas is killing two birds with one stone: shaping her into a more suitable dancer for the role, and preparing her for his relationship with her. He purposely abuses her verbally and sexually to cause a high stress level in her, hoping one day she'll snap. He just hadn't intended it to be so soon, before he could actually do anything with her.

His motive is to cover his own tracks. It's strongly implied that he seeks out sexual favors in return for giving dancers lead roles. The stress always gets to them, one way or another, and they snap. The authorities are less likely to believe the sexual harrassment accusations if they're mixed amongst the ramblings of emotionally unstable suicidals.

Lily really just wants to be Nina's friend without any ulterior motives.
Really I don't feel like Lily is ever mean spirited at any point, and always seems very supportive. She just seems like an amazingly nice, very genuine girl who wants to help Nina. Nina and her probably would make really good friends, with Lily helping her come out of her shell if it wasn't for the fact that Nina's pretty paranoid and decides Lily's after her. Lily didn't have to take such interest in her and try to to talk to her in the bathroom and she certainly didn't have to comfort her after her sexual harassment from the director. She even takes Nina's whole sex delusion pretty well, just teasing her about it and not even being weirded out or being cruel. The only point in the movie where we see(rather hear) anything mean from her torwards Nina is when Nina is half crazy and getting ready for the show, so that may have been hallucinated. Unless Lily is a master manipulator and damn good actress, I'm pretty sure she wasn't just playing to take Nina's role.