人类与机器共存的世界——完全被管制统治的“不需要感情的乐园”穹顶城市Romdo。在那个乐园都市里发生了谜一般的杀人事件，同时出现了被Cogito病毒感染的出现了自我思想的Autoreiv,负责追踪踪事件的市民情报局的年轻的职业女性莉露.梅亚在偶然中发现了有别于人类与机器人的怪物存在的秘密,，随后在她的居所的墙壁上出现了神秘的留言AWAKENING,并受到了怪物的攻击。

没有人相信莉露.梅亚所见到的，该事件被定性为STALKER(在日本称为病态的跟踪者)尾随袭击并制造了爆炸的时间，同时莉露的助手Autoreiv伊基关于此事件的资料也被消除，使得莉露确信了城市中发生的神秘事件与都市统治者之间定有关联，终于在一系列的调查下发现了PROXY的存在....与此同时，在商场中，移民青年文森特.罗被神秘的PROXY追逐着并且造成了大量市民的死伤。

因为卷入了神秘事件，无端被PROXY追杀，又被市民监管局通缉的文森特·罗自知当良民无望，偶然巧遇并是在Autoreiv皮诺的指引下，沿着通风口的回廊来到了Romdo出口处，虽被随后赶来的莉露竭力阻止，但在走投无路之下绝望的跃出了ROMDO。

PINO与小褔迪成为了朋友，经常一起画画. 莉露独自一个到ROMDO外面，想把LAW带回去调查。正好遇到ROMDO的自动巡逻机来攻击. 莉露被击中，为了捉住LAW而脱下了防护套，因此感染上重病. 福迪也在攻击中失去了生命。

由于一直生活在Romdo内，莉露在没有防护衣的保护下，感染了都市外的病菌，在医生的德莫西协助下而送回了理想都市Romdo。另外一方面，通缉犯LAW坐上了兔子(船)而往自己的故乡莫斯科前进。

Re-l recovers from her illness. Daedalus shows her the disturbing mechanisms responsible for the Dome’s continued survival. Vincent makes his way home, slowly losing his companions along the way, ending up alone with Pino. A group of infected AutoReivs is unleashed on Re-l, Iggy, and Daedalus. The episode ends with Daedalus filling out Re-l’s death certificate.

同行的旅人一个个死去，只剩二人的旅途因对故人的思念变得更加煎熬。无法再见到莉露的文森特在孤寂中前行，直到闯入战火弥漫的哈隆斯。然而这片满目疮痍的最后据点也没有他的容身之地，只有更多的杀戮和绝望。莫名的牢狱之灾，新的怪物的出现，疯女人如预言般的祈祷，这一切意味着什么呢？

皮诺和文森从哈隆斯的残骸中被阿修罗的城主卡兹奇斯-郝巴救出，来到了日出之国。徘徊在黑暗中的人谁都渴望光明，然而见到光明时却因炫目耀眼而无法直视，甚至感到痛苦。真相也是那样的东西。初始的友好随着事实的揭露迅速崩坏，文森的身世之谜终于展露出来。

警备局长鲁尔（rule）和医生迪达罗斯·梦想（dream）的对峙。充满了隐喻和代号的一集，每个人都在追寻自己存在的意义。rule自以为代表正义，可以控制摆布dream，可事实真的如此么。。。徘徊于虚拟之乡的莉露（real），拿出所有的觉悟，寻找这世界背后的规则（law）。

“欢迎光临城市之光书店”，前途莫测的vencint在这里面对自我（ergo）的循环拷问。要寻找的东西往往总是早已在心中，不能一次追求所有的东西。真正需要的是“接受”，不然就会在黑暗中迷失，也因此会失去真正重要的东西。终于接受了现实的文森特犹如书面上的蝴蝶一样完成了心灵的蜕变，也终于与莉露相遇。

The group is confronted by a vagrant Proxy and its companion AutoReiv, and Re-l puts her new weapon to use.

An infected Iggy becomes enraged and kidnaps Re-l, setting out to kill Vincent. Re-l is again confronted by the homeless AutoReiv.

While resting in a long-abandoned dome, strange occurrences take place and the trio’s lives are endangered.

Finding himself in a bizarre live game show, Vincent’s trivia knowledge is put to the test as he battles for his life.

When winds die out, the trio are stranded aboard the Centzon and Re-l finds herself struggling to hold on to her sanity.

Romdo is on high alert as they search for the fugitive Raul, who plans to activate a deadly weapon. Meanwhile, the trio discover strange humanoids living inside a toxic cave system.

The trio reach the devastated Mosko, Vincent’s home city, and find that the truths lead back to Romdo.

Pino explores the mysterious Smile Land with the NaKaMa, and confronts the Creator of the city.

Vincent finds himself trapped within Re-l’s consciousness, and observes powerlessly as events unfold.

A Cogito outbreak spreads through Romdo and the city falls into chaos. Vincent incites the people to revolt, pushing them to hunt down and kill all AutoReivs.

As the city continues to crumble, Vincent and Re-l encounter Proxy One. Raul is overcome with regret and despair, and sets out to find Pino.

Pieces are played and revelations uncovered as the final fight commences. Monad makes her return and tries to convince Vincent to join her.