The game beings with Shinji having a nightmare about Gendo being murdered.

A teenage girl has been possessed by an Angel and transformed into a dessicated, three eyed monster with tentacle arms. She attacks and kills several police officers and is attacking Rei when Shinji arrives on the scene to fight her off. Misato shows up during the battle and rams the Angel with her car, then chases her away. A Nerv recovery team takes control of the scene and the injured Rei.

The Angel is a shapeshifter, like The Thing. It takes the form anyone it attacks. After the fight, it shows up in the form of a smiling Rei with shadowed eyes. It appears at the school and kills one of Shinji's classmates, a Nadia look alike named Natsuko, and then transforms into her.

Fellow detective Kaworu Nagisa arrives on the scene and I think he accuses Rei of being the murderer based on DNA evidence. He says he's there representing Seele, and there's a graphic showing the relationship between Seele and Nerv.

Seele also appears to be a court of some kind. There are a bunch of podiums set up within the circle of monoliths. Suspects are called before them and the characters take part in Ace Attorney-style argument sequences. From what I can tell, Kaworu serves as the accuser/prosecutor and Shinji and Misato the defense.

Shinji is able to prove that Rei isn't the Angel, and that it's been masquerading as Aoi Mogami, one of the teachers at the school.

After being outed, the Angel takes on its true form, a black and white striped three-eyed giant that attacks by shooting tentacles out of the eye holes in its mask.

Misato takes Shinji back to Nerv and introduces him to Unit 01. He defeats the Angel in battle and the chapter ends shortly after.

I'm not sure what happened to the real Aoi. We don't see her after the Angel is outed, but she's never shown to be dead, either. Also, none of the Evas in this game ever use umbilical cables and they don't have a timer in battle.

Shinji gets punched in the face by Toji. They mention his sister, so I guess Sakura was injured in the battle with the stripey Angel. Some things never change, huh? Shinji tools around the school for a while until he and Rei happen upon Hikari, who has discovered a body!

Two more bodies are found later: A Nerv technician with their head smashed into a computer, and a music instructor with a broken neck. Poor Hikari is accused of being the murderer!
Shinji and Rei somehow figure out there is an Angel hiding in the music room that manifests in response to music and attacks its victims with some kind of sonic blast. Shinji plays his cello to lure it out, and a man-sized Eva 00 does battle with it.

I have no idea how or why Eva 00 is so small. The two Evas are deployed on the surface shortly after and they're both giant. Who knows!

Nerv plays the same song over the city's PA system to lure the Angel out of its cloaking coccoon, but something about its sonic attack disrupts the music and the Angel disappears again. Nerv goes back to the drawing board, and comes with a new plan: They redeploy the two Evas, but this time Unit 01 is equipped with a giant tuning fork! It causes the Angel to materialize whenever it's in range of the soundwaves.

As soon as they make contact with the Angel, Toji and Kensuke are found in the area and Shinji has to let them into Unit 01's entry plug. Unit 01's synch ratio is cut sharply, but Shinji and Rei defeat the Angel. Back at school, Toji lets Shinji pop him in the chops, settling the score. The case ends with Gendo speaking to Keel against a black backdrop.

The case begins with Gendo in his office, speaking about something. Meanwhile, at the school, Misato, Shinji, and friends have prepared a welcome for the pilot of Unit 02, which is being airlifted to Japan in the big carrier planes. In true Asuka fashion, she has the crew air drop her right in the school yard!
Kaji also debuts in this episode, delivering the embryonic Adam to Gendo's office.

Immediately after, a cluster of Angels shaped like bowling pins appear in Tokyo 3! The battle music winds up...but the bowling pins don't do anything, so the calm music comes back and the investigation begins!

The kids check out the Angels up close, talk to a few people around town, and speak to the owner of what I *think* is a bowling alley a few times. I'm not really sure what's going on in this part. But when they go back to check on the Angels again, they've multiplied! There were just three at first, but now there are nine!

The kids go back to the bowling alley, speak to some people and Shinji practices his bowling while Asuka provides color commentary. The earth shakes and an alarm blares, and the kids rush outside to see what's happened.

Kaworu's Eva, Evangelion Otsugata, has touched down on the street outside, looking like a boss. Some planes fly over the bowling pins and we get some aerial views of them, but still nothing happens, so it's back to the bowling alley.

An alarm sounds at Nerv HQ and there's a tremor of some kind. The bowling pins have multiplied again: there are ten of them now, all numbered with roman numerals and each of them with a face at the top of the pin. Nerv deploys Units 01 and 02.

Asuka rushes in and attacks the bowling pins with an EVA STUUUURIIIIKE! It seems to work at first, but the Angels regroup while Asuka's back is turned and dispatch the two Evas with a flash of light.
Shinji and Asuka scrape up the remains of their dignity, command regroups, and the Evas are sent back into action. There's a giant Nerv shellfish on the side of a building for some reason.

Command's plan: Use Eva 02 as a giant bowling ball! The battle is basically a bowling minigame: Unit 01 has to get the Angels into position and throw Unit 02 at them. Asuka doesn't seem 100% on board with this plan. And to make matters worse: Kaji is watching! Still, the plan is a success.

This case doesn't have as much action as the previous two aren't there aren't any murders this time around. It's mostly character dialogue so there's a lot I'm missing out on here.

The episode begins with Evas 03, 04, 05 (an MP Eva) in a cage, followed by Gendo and Fuyutsuki in an elevator discussing the Evas. The power goes out, and we're treated to these lovely images of a berserk Eva on the attack.

Evas 00, 01 and 02 are sent out in the carriers, and there's a long conversation between the Children and Misato that sounds like a mission briefing. Eva 03 is mentioned repeatedly, so I think it might be an activation test that went haywire. Also, this case doesn't seem to be set at NERV HQ. With the long flight and Evas 03 and 04 being involved, maybe it's one of the American bases?

The scene at the base isn't pretty. Unit 04 has a hole punched straight through it, Unit 05's head has been torn completely off, and Unit 03 is slumped in a heap, covered in blood but otherwise uninjured.

Ritsuko gives a breakdown of the Units, and it looks like Units 04 and 05 were going to run on Dummy Plugs. The team also finds two KAWORU.01 dummy plugs in one of the hangars. Shinji's confused to see Kaworu's name on them.

In the recovery ward, they meet...Toji! Toji was conducting a synchro test with Eva 03, but evidently something went wrong. The kids go outisde and talk amonst themselves, and Shinji seems really upset about something.

Asuka notices something in the sky. It's Otsugata, leading a squad of Seele's flying monkies. The MP Evas are set as guards over Unit 03, which is restrained on a giant red cross. It seems that Seele wants to take Toji and Unit 03 into custody in light of the debacle.

Shinji retires to his room, and when the group comes back to the hangar where the Evas were, the MP Evas have all been destroyed. Such a tragedy, really. Unit 03 is covered in blood, but it's still on the cross.

One of the MP Evas is still impaled on a fake Lance of Longinus. WHen Asuka moves to pull it out, there's a flash of light, the fake Lance glows red, and Asuka begins freaking out. She attacks Unit 01 while repeating this phrase over and over: http://imgur.com/cWEAesa

Shinji manages to defeat her. The fake Lance crumbles to dust and Unit 02 collapses, but Asuka's unharmed. Unit 03 is put back in its regular restraints, and the other four Evas...sit around a campfire in the hangar?

Unit 03 is found slumped against the wall of the cage along with the remains of two more dead MP Evas. One's been torn in half and the other dismembered. The investigation of the wrecked Evas turns up something strange. It's either a bite mark on the Eva's armor or a dark splotch in the blood underneath it. Either way, Nerv decides to take a closer look at Eva 03.

They pry its mouth open and find a dark splotch hiding in a cavity in one of its molars. Doctor Shogoki pulls the tooth out (while Toji is synchronized!) and the dark splotch reveals itself as a tiny black Angel holding a pitchfork! It's been taking control of Eva 03 and making it attack the other Evas. It's very strong and fast for its size, but the three Evas chase it down and stomp it into paste.

Toji got roughed up somehow and is being loaded into an ambulance at the end, but otherwise he seems fine! The case ends with Keel talking to some mysterious voices. Overall it's a fairly light and silly case. There's a lot of bloody Eva carnage, but nobody's really hurt except for Toji.

Case 5 is where things take a really dark turn. Kaji leaves a long message on Misato's answering machine, which is never a good sign. Right after, we see what's become of poor Kaji, and it is not pretty. He's been crushed to death by a giant hand.

Kaworu delivers the news to Nerv, and the kids and Misato go to investigate. The kids are devastated. Poor Asuka breaks down into tears. Shinji is stunned, and Misato tries her best to put on a strong face for their sake.

The camera pulls back to reveal the hand print, which really narrows down the possible suspects. The kids go to the Eva cages, and with Maya's help, they check Unit 01's hand, which has seeds pressed into the palm!

They meet up with Kaworu, who says something to get under Shinji's skin, and then the three kids regroup at Shinji's place. There they meet with Hyuga, Aoba, and Maya, who help them set up a remote link to the Magi through a laptop, and together they start digging up info on the Second Impact. They find some information linking Gendo to it and they discover that Misato was a survivor, but as they try to pursue further leads into Misato and her father, they run into dead ends with missing or restricted information. Red flags start going up, and Ritsuko's name is thrown around.

Shinji, Asuka and Rei meet Kaworu and Misato in Gendo's office. Gendo is being taken into custody! The next day, there's another Seele court sequence. Apparently Gendo is being accused of using Unit 01 to somehow kill Kaji.

This Seele sequence is very long with very little material that I can understand. Partway through, Ritsuko is called in and Misato immediately goes on the offensive. What I can gather is that Ritsuko is outed as Gendo's accomplice, Kaji is outed as a triple agent, Gendo starts turning the guns on Seele, and everything is coming to a head.

I wish I could understand what they're saying in this part, because it seems extremely fascinating. The kids and the three operators seem to be on the verge of uncovering the whole Seele conspiracy and Second Impact is thrown right into the open. Gendo and Ritsuko are both still free at the end of the case, so I'm not sure how Kaji's murder is resolved.

Continues off of Case 5 and shit really hits the fan. It begins with Misato having a flashback to Second Impact while a music box version of Cruel Angel's Thesis plays. There's a picture of Adam's wings and someone yelling about an Anti-AT field. Then Misato thinks about her father and Kaji for a bit. Kaworu takes over the voiceover and talks about Second Impact and Shinji.

We hear the sound of something collapsing, and we find that Gendo has been killed by falling rubble in what I think is his office. The upper part of the pyramid has been destroyed by something.
Shinji and Misato meet up in Unit 01's cage later and have a long talk, when Kaworu shows up with some section 2 agents and...Misato's father! Misato is completely floored, and I can hardly blame her. Shinji is comforted by Asuka and Rei, then goes to visit his father's body in the morgue.

He has a talk with Maya and Ritsuko, and goes to visit Unit 01's cage. He starts punching Unit 01's foot, yelling at it, when Unit 01 activates and grabs him! Unit 01's plug ejects and there's some chatter on the bridge about a 200% synchronization rate. We next see Shinji inside the plug tripping balls, so Unit 01 must have put him inside. His synch rate rises up to 400 and he's absorbed inside the Eva.

Inside Unit 01, Shinji has a vision of the LCL sea from Instrumentality and speaks with Kaworu. They talk, and Shinji gets angry at something and rejects Kaworu. They start to fight, then come back to their senses once they get it out of their system. Shinji reappears bare naked and I have no idea what the hell just happened. Shinji meets up with his friends on the bridge, and they head back to Seele as the case ends.

This is a lot of Seele court. Dr. Katsuragi and Misato take the stand and are grilled about Second Impact. Seele's role in the disaster becomes more and more clear and it looks like Shinji, Asuka and Misato even start accusing Keel directly. Ritsuko shows up near the end of the proceedings, and there's some kind of explosion. Shinji, Asuka and Rei pursue Ritsuko back to Nerv on Misato's orders and confront her on the bridge.

Ritsuko puts a gun to her own head. They talk about Gendo, Kaji, Seele, Second Impact, and Third Impact and then Ritsuko kills herself with the gun. Her body lands on the lower level of the bridge, almost perfectly mirroring her mother's suicide.

The kids meet up with Misato and her father outside and report what happened. Misato's upset to hear the news, but things immediately get much worse. Misato's father starts gagging and groaning and howling. He rips his shirt open to reveal that he has a core on his chest! And somehow they're able to detect that he has an S2 organ as well. Misato draws her gun on Dr. Katsuragi, but there's nothing he can do at this point. I think it's implied that Ritsuko knew about this and it's one of the reasons she killed herself.

In one of the cruelest twists I've seen, Misato's father transforms into a giant thre-eyed Eva/Adam-esque being and goes on a rampage. Shinji is extremely reluctant, but Misato orders the Evas to launch and they're forced to kill him. Shinji and Misato are both in tears. Shinji can't stop apologizing, but Misato thanks him herself and apologizes to him.

The voice actors did an amazing job selling the agony and the heartbreak in this scene. It's incredible.

Misato and the kids meet with Fuyutsuki in the commander's office to discuss what's coming next and the plans that were in action. Seele's plans took a hit with the destruction of the Eva series, but Kaworu suddenly takes control of Evas 00 and 02 and begins his descent into Central Dogma just like in NGE. Unit 01 pursues him into the shaft and engages the two rogue Evas in a battle sequence. They tumble into Terminal Dogma, and Shinji catches Kaworu before he's able to merge with Lilith.

There's a fake-out that makes you think Shinji killed him just like before, but instead Shinji drops him iinto the LCL pool. Even Kaworu's confused about being alive! While they're talking, Eva Otsugata drops in from out of nowhere, scoops Kaworu up and eats him with no preamble. Evidently this was part of Seele's plan all along. Asuka and Rei regain control of their Evas and engage Otsugata in a boss fight.

After they defeat it, Otsugata's AT field starts going haywire. It sprouts wings and is engulfed in a sphere of feathers before shedding its armor and transforming into some kind of Awakened form that has four wings and a halo. There's a flash of light and Dogma is transformed. Lilith, the platform and the LCL sea remain, but there's a ruined city off in the distance and the roof is replaced by a stormy sky with a swirling vortex in the center. It's oddly similar to NTE's new Impacts.

Another boss fight follows and Otsugata is destroyed. It vanishes in a pillar of light, and Kaworu floats down into Unit 01's hands to deliver some parting words to Shinji before dying.

There's a brief time jump after Kaworu's death. Asuka, Rei, Hikari, Toji and Kensuke all stand around Shinji's desk at school, clearly worried about him. The door to the classroom opens, and Shinji steps in, greeting his friends and comrades with a big smile before the credits roll.