The story of MegaTokyo is long and complex. Here is a brief overview of past events to help refresh the memory. Be warned, there are spoilers here.

Chapter 0: Relax, We Understand J00

Piro and Largo, two American gamers, travel to Tokyo on a whim and find they can't afford tickets home. They hook up with Piro's friend Tsubasa and move in with him. On an excursion into the city, Piro is confronted about his choice of reading material by a young schoolgirl named Sonoda Yuki. After Piro flees the scene, Yuki finds Piro's bookbag - and his sketchbook. Depressed about his failure to find his lost bookbag, Piro helps out a young woman named Nanasawa Kimiko who doesn't have enough money to buy a rail card and walks off before she can thank him. Piro lands a job at the MegaGamers store when a woman named Hayasaka Erika (who happens to be Kimiko's friend and roommate) abruptly hires him. Piro's conscience Seraphim, who is trying to help Piro work through his problems, is sent an assistant to take charge of Largo - a hamster named Boo. Largo runs into a spooky young woman named Tohya Miho, senses evil in her, and reacts accordingly. Tsubasa introduces Piro to Ping, a prototype robot girl and console accessory for dating simulation games. After being convinced by Ping to search for his childhood love, Tsubasa suddenly departs for America, leaving Piro and Largo no place to stay and Ping to take care of.

Chapter 1: Do You Want To Save Before You Quit?

While trying to track down t3h 3vil girl from yesterday, Largo finds himself hired as an English teacher for her class. Ping also joins the class, and is immediately befriended by Miho, who notices that she is a game accessory. A nervous Yuki returns Piro's bookbag to him at MegaGamers, and yells at Piro for not thinking his artwork is any good. After school Largo meets Miho and Ping at a local arcade where a massive showdown ends in a draw. Piro arrives in the aftermath, and Miho realizes that she knows him. Kimiko, who had recognized Piro in the store the day before while visiting Erika, decides to bring dinner to Piro at his new home in the apartment on the third floor of MegaGamers. She is dismayed when Ping answers the door wearing only a t-shirt, and leaves thinking that Piro might not be such a nice guy after all. Container ships burn off the coast as Ed and Dom arrive in Japan.

Chapter 2: Things Change Little By Little...

Faced with rioting students who are demanding the return of Great Teacher Largo, Shiritsu Daitou High School sends Junpei to bring Largo back to teach his class. Kimiko auditions for the voice role of "Kotone" in a game called "Sight." Asmodeus shows up to tempt Piro and sabotage Seraphim's work. Miho mysteriously faints in the bathroom and Ping watches over her as she recovers in the nurse's office. Ed, whose mission it is to return Ping to the Sony labs, finds her but is thrown out the window when he tries to 'retire' her. The explosion caused by Ed's landing opens an inter-dimensional rift, unleashing an undead horde upon the city. Dom helps Largo fend off the zombie attack before the Tokyo Police shut everything down due to improper permits. Yuki returns to MegaGamers and asks Piro for art lessons. Later on, Erika startles Kimiko by inviting the boys out for drinks at a beergarden. As Largo details the day's exploits to to her, Erika watches as an inebriated Kimiko yells at an equally inebriated Piro. The night ends as Erika and Largo carry their unconscious roommates home.

Chapter 3: Am I Your Number One Fan?

Largo takes his class to an arcade to sharpen their skills, but loses a duel to Miho. Piro visits Kimiko at the Anna Miller's restaurant where she works. Largo is apprehended by Inspector Sonoda Masamichi (Yuki's father) but the arrest is interrupted by the attack of a giant, drunken monster turtle. Largo cleverly uses Ping's strength to fend him off which impresses the Inspector, who hires him to be a Special Contract Operative for the Tokyo Police Cataclysm Division. Kimiko learns that she has won the role of Kotone in the game, "Sight." Piro gives Kimiko a drawing he had done of Kotone, one of his favorite characters. Piro forgets Yuki's art lesson as he does "research" to figure out what to do next about Kimiko.

Chapter 4: Low Ping Rate

Miho takes Ping and the boys out to a public bath and then to a restaurant where she reveals herself as their old nemesis from an online roleplaying game. Seraphim is captured by Asmodeus to prevent her from meddling with his plans to get Piro to loosen up and have more fun in Tokyo. Back at MegaGamers, Dom confronts Erika about her former idol singer career that she had abruptly abandoned, leaving her fans wanting more. Largo fends off a probing attack by fanboys in the digital plane and physically removes one who came to see if the rumors about Erika's whereabouts are true. Boo comes to the rescue and battles Asmodeus, but Seraphim is injured in the attempt. Yuki's brother Yuuji confirms that Erika is indeed the long missing Idol.

Chapter 5: Color Depth

A crowd of Erika's fans assemble outside MegaGamers. Largo brings his class to help fend them off. Erika prepares to face the mob, but Ed's new attempt on Ping's life shatters the area. Erika and Piro go outside to check on the mob's safety but retreat back inside when Piro is injured. Inspector Sonoda disperses the mob and explains the power idols have over the public and how Erika is still quite 'dangerous.' Kimiko frets over Piro who initially tries to hide from her but then faces his fears and goes to talk with her. Yuki, who has arrived for her lesson, leaves when she sees Piro and Kimiko's obvious concern for each other. Largo finds Erika curled up and depressed in the break room and works to cheer her up by challenging her to a video game.

Chapter 6: Operational Insecurity

Largo convinces Erika that she can better handle her fans if she monitors them online and gives her computer lessons. He follows her as she goes out to buy parts to make her own PC. They run into Sonoda Meimi, Yuki's mom and a woman Erika looks up to, who mistakes Largo as Erika's new boyfriend. A confused, bitter and conflicted Erika harshly tries to drive Largo away, but it backfires as Largo tells her that he refuses to play that game and leaves. Piro, depressed by how well Largo seems to be doing with Erika and how poorly he feels he is doing with Kimiko, blindly follows Ping to the Cave of Evil nightclub which Miho has invited them to record Kimiko's first radio appearance. Largo, who has drowned himself in beer, follows them. After being confronted by Ping and unable to hear Kimiko's show, Piro returns to the main floor only to find Miho cruelly messing with Largo. He confronts Miho and drags his friend out of the club. Kimiko's publicity appearance on the radio show doesn't go well after she scolds the hosts for badmouthing fans. All this is forgotten as she tries to help Piro get a drunk and skittish largo home. Kimiko and Piro talk openly for the first time as Piro finally understands that constantly tearing himself down only hurts the people who care about him.

Chapter 7: Known Bugs and Security Flaws

After building a makeshift computer for Piro, a still depressed Largo walks aimlessly through Tokyo. He encounters Junko, one of his students, who follows him into the arcade and restores his mood by forcing him to play a video game match against her, followed by some advice on dealing with girls. Piro hears from Tsubasa over online chat that Kimiko’s popularity has skyrocketed overnight. Yuki arrives at MegaGamers and finally gets her first art lesson from Piro. Erika’s fans again crowd the store, Miho shows up and causes a scene, and Dom also appears in order to offer Erika protection via employment with Sega. Largo makes a triumphant entrance and clears the fans out with Erika’s permission. Ping picks up Miho to save her from his assault but loses her balance and drops her, Miho is saved again by a fast moving Yuki. Masamichi comes to the store and is horrified to find Miho there. She reveals she once got into trouble doing something with Erika’s fans, then leaves. As Erika and Masamichi talk, the horrible truth comes out: when Erika was engaged to his brother Sonoda Hitohsi, Hitoshi lied to them both to keep Erika from meeting Yuki and Yuuji before dumping her completely. Largo tries to console a devastated Erika with the story of his and Piro’s online battles with Miho, ending in a disjointed moral that emotional attachments lead to trouble. Miho prevents another of Ed’s attacks on Ping. Kimiko, against the advice of both Piro and “Sight” producer Matsui, goes to work her shift at the Anna Miller’s depsite the crowd of fans waiting for her. Piro follows and tries to help but only makes things worse. Afterwards, Kimiko is distraught over the whole thing and takes it out on Piro, but she goes too far and he walks out on her.

Chapter 8: Defect Mapping

Erika forces a depressed Kimiko to face her day, then gets Largo to take her shift while she assembles her computer. Miho stops by and reveals to Piro that she saw how upset Kimiko was the night before, but Seraphim reassures Piro that he was not at fault. Erika calls for help with the PC, but Largo has left to teach his class and Piro goes in his place. After a severe scolding from Matsui, Kimiko storms out from the “Sight” studio. She returns home and hides when Piro arrives, then dashes out when she overhears that he hasn’t given up on her. Ed attacks and is defeated by Miho at the school, the resulting explosion sets Ping into a crying fit that she can’t stop. Miho demonstrates that Yuki is a magical girl by leading her up onto the power lines, but Yuki loses her balance and falls off. Largo, Piro, Ping, and Kimiko meet up back at the store. Ping’s problem is traced to her emotion programming correcting errors. Piro and Kimiko make up and fall asleep watching television together. Largo solves Erika’s PC problem and brings his own PC over there for a shakedown round of gaming, which ends when Erika tries to get intimate. Largo returns to the MegaGamers apartment in defeat.

Chapter 9: Overlo4d

Kimiko leaves and Piro reassures Largo not to worry about his embarrassment with Erika the night before. Dom, Ed, and Miho converge on Kimiko, Miho grabs Kimiko and runs just as Ed launches an attack. Dom follows and offers Kimiko protection via employment with Sega, which she refuses. Piro learns via Kimiko’s fans that Miho is with her and runs out to find them, but is intercepted by a group of Kimiko’s fans that seek to help her. Yuki visits her classmate Yutaka in the hospital, having fallen on and injuring him, then afterwards encounters Piro and follows him to his meeting with the fans at a maid cafe. Kumakuma, a masked “Sight” insider, explains that the game has lost funding and fears Kimiko’s reaction. Miho, moved by Kimiko’s philosophy, travels with her to the “Sight” studio where they also learn the bad news but decide to go through with a planned promotional event anyway. Zombies invade the city again, and Largo journeys out to combat them. He finds and teams up with Yuki, and they pick up a Rent-A-Zilla as well. The zombies head towards the event, Yuki and the Zilla hold them off while Largo moves into the crowd of fans. Piro’s group arrives as well and Piro chases after Largo while Kumakuma, revealed as character designer Sayuri, takes a secret entrance into the event. The fans bring Piro and Largo up to the event as well, but Largo leaves again when Miho hints that Yuki needs help. The Zilla has become a zombie and is under attack from the Tokyo Police. Yuki uses her powers to save him and takes him home with her. “Sight” receives new funding from Dom. The event finishes and everybody gathers outside, but Miho goes off alone and is caught in a massive attack set by Ed.

Omake Theater: Grand Theft Colo: Otaku City

Makoto the MT server is kidnapped and on the run from all sorts of shady characters.

Omake Theater: Circuity

Piro helps an injured Kimiko while Largo searches for Erika.

Omake Theater: unMod

Piro and Largo receive unexpected interference from Yuki while on a mission to thwart a girl trafficking ring.

Omake Theater: Full MegaTokyo Panic! Clan'd War3z

Piro and his team infiltrate a school to protect Miho from Piroko.