Numbered the chapters for the sake of convenience. All the chapters begin the same way, with the various protagonists breaking the fourth wall and introducing themselves directly to the player. They also break the fourth wall periodically during the actual game, asking the player questions like "Who are you?" and "How long do you plan to keep watching me?" This is relevant.
Chapter 1 - Haneda Takeshi / Hawk
We meet Takeshi, a stoic and rather nerdy high schooler with no real friends. However, he's forward-thinking to the point of it being downright pitiful, and does a marvelous job of convincing himself that the people bullying him are just trying to be nice. He used to hang out a little with a classmate called Morisato Kazuma. Kazuma was basically making fun of him the whole time, but Takeshi assumed--made himself assume--Kazuma had only the best of intentions.
Back around the same period, he and the beautiful but aloof Watarai Asuka made a deal: they would pretend to be going out so male students would stop bothering her. Even after agreeing to this, they almost never had a single conversation, but several years later, they still haven't publicly broken up. Other girls Takeshi meets or interacts with in this chapter include his little sister Haneda Kobato, who acts very quiet and diffident around him, like she has no idea how to treat him, and Yamashina Miyako, another semi-outcast.
If Takeshi comes under emotional strain--in times, for instance, when he really struggles to maintain the illusion that those around him aren't secretly mocking him and don't mean him harm--he escapes to a hilariously stereotypical fantasy world where he is a god-like hero. In this world, Asuka is the princess he serves, Miyako is a witch, and Kazuma really is his faithful comrade. According to the world's mythology, Takeshi/Hawk is one of four great heroes who have scattered and now seek to be reunited--him, Eagle, Falcon, and Garuda.
Takeshi honestly believes, at least on some level, that he is the Earthling reincarnation of this legendary Hawk person, and that whenever he escapes into his delusions, he is getting summoned back to the world he truly belongs in. He sees golden sparks drifting each time he gets summoned. There are also quite a few occasions where he wakes up on Earth after being summoned in a completely different place/time than before--like suddenly opening his eyes to find himself in the bathtub. The chapter ends when he undergoes a particularly traumatic event and escapes again instead of facing reality.
Chapter 2 - Chitose Shuusuke / Eagle
After a brief and cryptic intermission framed as a radio show from the abyss, we shift to Shuusuke's POV. He moves in completely different circles from Takeshi, and he has a lively, outgoing personality. On the surface, he very much seems like the class-clown type, but he is in fact very sensitive to others' reactions and always cracks jokes and keeps smiling to make everyone else at ease. The result, though, is that while he ends up as the life of the party, and people like him, no one really takes him seriously, and he has to work hard to maintain his image.
If Takeshi is a "student"--in his chapter, we only ever see him at school, getting ready for school in the early morning, or going to bed late at night--then Shuusuke is a "freeter," which basically means someone who scrapes by via part-time jobs, never sticking with any one thing for long. At first, we mostly see him hanging out at Alexander, his favorite coffee shop, which features a cool-looking but ridiculously perverted shopkeeper, pretty waitresses with sharp personalities.... and perhaps most importantly, Ohtori Kakeru.
Kakeru is another Alexander regular, described as being absurdly tall and good-looking. He's an up-and-coming artist with a cruel tongue who usually acts cynical, bored, sarcastic, or a poisonous mixture of all three. He uses Shuusuke to amuse himself, but for the most part, they get along quite well. Whenever the store closes and everyone goes home for the night, Kakeru heads off in the opposite direction. No one knows much about his personal life, except that he goes through women like tissue.
Shuusuke eventually accepts an on-and-off job at Alexander. Around the same time, a high school girl called Tamaizumi Hiyoko also joins the staff. She previously debuted as a young novelist to great acclaim (and sales), but her more melancholy second work turned out to be a flop, leaving her touchy and depressed about her writing. She gets a very bad first impression of Shuusuke, but he quickly becomes attracted to her.
The rest of the chapter consists mostly of comedic hijinks wherein Shuuske keeps accidentally looking worse and worse in front of Hiyoko. However, there's a more unsettling underlying thread: he hears rumors that Kakeru is carrying on a double life as the leader of a violent gang. One of his employers, an editor at the company that publishes Hiyoko's novels and is affiliated with Kakeru's work, asks him to bring Kakeru back to the straight and narrow.
The only connections between Shuusuke's chapter and Takeshi's, which came before it, is that Shuusuke makes extremely brief references to knowing Takeshi and Kobato (and even more briefly, Hayato). There is also a scene where he runs into Kobato on the street, and she acts surprised, but polite.
Chapter 3 - Narita Hayato / Falcon
After a break for another radio show from "the abyss," it's Hayato's turn. While we mostly see Takeshi in the morning and during the day, and Shuusuke during the late afternoon and evening, Hayato's chapter takes place almost entirely at night. His acquaintances even call him "Dora," short for "Dracula."
Note: Hayato's chapter is extremely long and involved, with a huge cast of colorful side characters. As interesting as they are, it would take forever to write about, so I'm going to cut the side plots. Just know that one major theme of Hayato's storyline is how he stops holding other people at arm's-length.
Like Shuusuke, Hayato makes oblique references to knowing him and Takeshi--as well as a hitherto unmentioned person called "Youji"--but at first gives no clue as to how all of them are acquainted. He, too, is familiar with Ohtori Kakeru, but the Kakeru he knows is the polar opposite of the one Shuusuke is friends with. The Kakeru who Hayato meets is crazily energetic, dangerous, prone to violence, a matchless fighter, a flashy dresser, and the charismatic leader of a gang called the Flame Birds. Among his loyal followers is Morisato Kazuma (aka Takeshi's former classmate).
Kakeru is fascinated by Hayato, although it's unclear exactly why--aside from the fact that Hayato, too, is a skilled fighter. He received some martial arts training from a priest who looked after him when he was a child. There are a number of flashback scenes where the priest asks him why he keeps getting into fights, and he responds angrily, saying that he has to stick up for Takeshi and Shuusuke, because they aren't capable of defending themselves against bullies. In exchange for teaching him how to fight properly, the priest makes him work on his anger management issues. He teaches Hayato a mantra to cool his head whenever he risks losing control: "May there be world peace."
Incidentally, this is the same mantra Takeshi often repeats to himself when he's in upsetting situations. Shuusuke mentioned it once or twice in his chapter as well.
Since Kakeru semi-stalks him, Hayato frequently ends up running into the Flame Birds and their friends--including Kouda Ai, a cute Valley Girl type who happens to be Kazuma's childhood friend. Kazuma has clearly been in love with her for a long time, but she only sees him as a friend, so he keeps his feelings hidden. However, she constantly flirts with Hayato, to the point of practically throwing herself at him. This only escalates over time. Meanwhile, Kakeru--who Kazuma hero-worships--is obsessed with Hayato, so Kazuma can't help but have pretty mixed emotions about him.
The main rival of the Flame Birds is a Goth gang called R-Wing. Hariu Kuroudo, who goes to the same school as Takeshi, is ostensibly their leader. He doesn't really have much to do with them, though. A talented musician and street fighter, he finds Kakeru rather exasperating, but Kakeru is just as in love with him (so to speak) as with Hayato, and is constantly trying to provoke him into fighting. It was mentioned in the Takeshi chapter that Hariu is related to Watarai Asuka.
Hayato takes odd jobs and occasionally performs heavy labor (such as night construction). It's through this that he meets Ohtori Naru, who requests that he help her find her stolen bicycle. She's actually Kakeru's little sister, but she and Kakeru have lived separately since they were children, and she isn't aware of his alternate identity as a bloodthirsty gang leader.
Naru is intimidated by Hayato at first, but she soon realizes that his gruff front is just that--a front. They occasionally meet up to look around for her bicycle and such. Fast-speaking, shy, and a little eccentric, Naru usually has a hard time getting to know people and talking to strangers, but she's oddly comfortable around Hayato. After a while, it becomes apparent that she's suffering from anxiety about the prospect of going to school--where, due to various events, she has no real friends--and has been skipping classes for a long time now.
In Hayato's chapter, we get the biggest reveal of the game--namely, Hayato, Shuusuke, and Takeshi aren't separate people. They're all distinct personalities in the same body. Takeshi wakes up in the morning and goes to school. In the evening, Shuusuke takes over to work at Alexander and hang out with his friends. At night, control switches to Hayato, who roams the city and performs his odd jobs.
Takeshi has no idea that he has dissociative identity disorder. Whenever the other personalities take over, he thinks he's been summoned to his mythical fantasy land. (It also becomes clear that this fantasy land is based on an RPG video game which almost everyone of his generation played as a child.) He's described as the third personality. Shuusuke is the fourth, and Hayato is the fifth, but they were "born" around the same time. Unlike Takeshi, they know that they are personalities sharing the same body, and have arranged a delicate balance in terms of dividing their time and covering up for each other (since each of them has a different circle of acquaintances).
The original personality has been the mental equivalent of a hikikomori for years, refusing to come to the forefront.
Shuusuke and Hayato promised the priest that they would work to earn as much money as possible so that Takeshi could live on his own after graduating, and no longer impose on his aunt and uncle. They both hope that Takeshi--the only one among them who has a chance at a real future as an upstanding adult citizen--will then rise to the occasion and take control, or merge with them.
As the turf war between the Flame Birds and R-Wing escalates, Hayato tries (and fails) to remain perfectly neutral. Someone starts targeting all of his close friends and associates, including Kouda Ai. When he is given a picture of her with her bra and underwear exposed, saying that R-Wing is holding her hostage, he almost loses his cool for the first time since the priest warned his childhood self not to fall prey to anger.
When Hayato reaches the verge of being completely consumed by rage, the destructive and vengeful second personality--Itami Karura--tries to seize control. Hayato succeeds in driving Karura back. However, he learns that the reason Kakeru was so interested in him all along was because Kakeru once met and became completely enchanted by Karura. Kakeru underwent horrible physical and sexual abuse as a child--which is the most frequent cause of dissociative identity disorder--but he didn't develop the disorder.
As a result, he resents, envies, and admires Hayato & co. For years, Kakeru has received huge sums of money by blackmailing his wealthy father--who seems to be connected to his abuse in some way--and used much of that money to develop a drug that let him create a separate personality. Hence the difference between how he acts around Shuusuke and Hayato.
Hayato also learns that Kazuma, too, knew about his multiple personalities all along--of course, since Kazuma met him as Takeshi long before meeting him as Hayato. However, Kakeru ordered Kazuma not to say anything about it. Kakeru has one last go at trying to provoke Hayato enough to unleash Karura, but this time Hayato doesn't lose control. Additionally, Hayato discovers that Kazuma is the one who set him up and sent him the photo of Ai (who is unharmed); Kazuma felt, rather justifiably, that Hayato was stealing everything from him, from Ai's love to Kakeru's attention.
So the situation with the Flame Birds and R-Wing gets more or less resolved. Naru tells Hayato that the real reason she wants her bike back is because her old pager is in the basket--the only way her estranged mother can get in contact with her. Quite comically, they realize that they assumed the bike had been stolen all along, but in reality, it had been carted off by the city for being illegally parked. Oh, and by now they're going out and stuff, with Kakeru's blessing, but the progression to that point takes place quite smoothly and with no drama or angst, in counterpart to all the violent/dramatic gang-related stuff.
Chapter 4 - Itami Karura / Garuda
But. Just when everything seems to have calmed down, Karura--who has been awakened, as it were, by Hayato's recent spate of fury--takes over. Karura is the second personality. Each of the personalities has a different purpose, and his is to destroy, to kill, to lose control. He believes in the myth of Takeshi's fantasy world, and so even in real life, he's convinced that the city before him is the sad aftermath of the fantasy land he once knew.
Karura's chapter was my favorite by far. It's both hilarious--the other chapters had me smiling from time to time, but this one actually made me laugh until my stomach hurt--and heartbreaking. The hilarity mainly stems from the fact that Karura is so delusional, and constantly talks in very formal, kingly, medieval speech. Karura happens to be in Kakeru's company when he assumes control, so Kakeru--who is over the moon, of course--assumes the role of his liege.
We realize that Kakeru likes Karura because Karura is so completely insane. He envies the fact that Karura is living in a constant delusion, with no need to face reality. However, he's also amused by the ridiculousness of Karura's delusions. He tells him that he'll try to grant his every desire. The first thing Karura wants to do is commit murder, but Kakeru warns him that this might not be such a hot idea, so Karura settles for, er, ejaculating. (He peeked in on Naru and Hayato's ero-scene in the previous chapter, and his curiousity was piqued.)
It starts to become evident that as high and mighty as Karura talks, and as dangerous as he seems, he hasn't been in control of the body at all since childhood, so his personality is a broken mixture with some very young emotions and ideas mixed in. For instance, even as he narrates in LotR-style medieval prose, there will be occasional parenthetical asides where he reverts to using "boku," and simple language, saying things that clearly don't fit with his fantasy-world illusion.
Kakeru takes him to some high-class prostitutes, which results in possibly the best-written ero-scene I've ever seen. It is absolutely essentially for the plot, hysterically funny, and deeply, disturbingly sad. The drugged-up prostitutes administer to Karura fervently, but far from getting an erection, he starts to become terrified and panicked. He tries desperately to hide his fear and finish the job, because he doesn't want to look bad in front of Kakeru, but there are lines suggesting that his sex phobia stems from the fact that his mother raped him when he was little.
Afterward, Kakeru arranges an encounter between Karura and an R-Wing member. Karura completely wastes her, but in an obviously deranged manner--while stabbing her in the face with a broken bottle, he doesn't even realize that the red stuff coming out is blood. Kakeru then brings Hariu over. At first Hariu assumes Kakeru is just wasting his time again, but he too becomes amused and entertained when Karura starts babbling on about the setting of the fantasy world he thinks he's in, and so forth.
At night, Kakeru drops Karura off at Takeshi's house. Karura goes inside and meets Kobato, who asks him who he is. This confirms that Kobato (and Takeshi's foster parents) have been aware all along of the multiple personalities. Kobato does a surprisingly good job of coping with Karura, who reveres her as a princess and is willing to do anything she says. However, when Karura asserts that he has no intention of turning the body over to any other personalities ever again, Kobato becomes furious and tells him to let her meet her real brother--the original personality.
Chapter 5 - Haneda Youji / Condor
We go to the internal "abyss" where Youji, the original personality, has been hiding for years and years. The abyss radio that appeared in earlier chapters is in fact the imaginary radio Youji often listens to. Karura has found a new purpose for his rage--instead of directing it outward, at others, he will direct it inward, to grant Kobato's wish and drive Youji back to the surface. Youji, still a child, is scared and doesn't want to emerge, but Karura forces him out.
Youji is in the same body as Hayato and the others, but he thinks he's a little boy. Caught between his childish thoughts and adult desires, he semi-assaults Kobato, who goes along with it because she pities him. It's suggested that the reason Youji's multiple personalities developed in the first place was to protect Kobato from his mother, who mistreated her. He offered himself instead, so Kobato wouldn't be hurt, but his original personality couldn't take the abuse--and it's implied that he eventually murdered his mother.
When Youji comes face to face with the fact that years have passed since he first became a mental hikikomori, he can't deal with it, and he retreats back to the abyss. Karura, of course, becomes quite pissed off at him. Youji realizes he wants to go back to the surface for Kobato's sake, so she won't be lonely anymore. However, he thinks he and Karura should recombine, so Karura won't vanish into the abyss afterward. They need help to accomplish this, and they turn to the player--the silent witness who has been watching the events all along, the "last personality."
Karura asks whether you will lend them a hand or refuse to help. However, your only option is to refuse (presumably the other will become unlocked after you finish all the routes), and the two of them are doomed to remain in the abyss forever.
Final Chapter - Narita Hayato / Falcon
Which takes us back to Hayato. Takeshi has become increasingly delusional, spending less and less time in the real world, and things aren't going so well for Shuusuke. Tired of sacrificing himself to make sure everyone else gets along in his job at Alexander, he eventually quits. He and Takeshi end up yielding permanent control to Hayato, who has found a new reason to keep existing--namely, Naru.
There are some more sweet scenes with Naru, as well as scenes tying up most loose ends with all of Hayato's many acquaintances. Kakeru is disappointed that Karura has left (he tells Hayato that even Shuusuke is more entertaining than him!). He amicably disbands the Flame Birds and begins to spend more time on his job as an illustrator, telling Hayato that someday he's going to be world-famous. Knowing Kakeru, it seems quite likely to happen.
There's also a very amusing scene where we see Naru and Kakeru interact face-to-face for the first time in the game. They care about each other deeply and are actually much closer than either previously let on, but they feel obliged to put up a mutually tsundere front when others are around. On a similar note, Hayato--who was never very close to Kobato--resolves to start acting more like her big brother, since he's the only personality left now.
The epilogue after the credits takes place a year later. Kazuma, who got kicked out of the Flame Birds around the time when he tried to set up Hayato, ended up devoting himself to studying and working hard enough to get into college, where he's leading a colorful social life. Ai and Naru have resumed going to school (Ai still has regrets about Hayato, but she at least pretends to have moved on). Hayato has assumed a steady job, and of course he and Naru are still together. Happy end.