In the Roppongi district of Tokyo, high school student Shu Ouma encounters a wounded girl named Inori Yuzuriha, the vocalist of a popular internet group Egoist, taking refuge at his film club's workshop.
Shu follows the coordinates of Inori's robot to a drop zone where he meets Funeral Parlor's leader, Gai Tsutsugami, who asks him to safeguard a vial.
As the Anti-Bodies begin attacking the Roppongi area looking for the vial, it shatters as Shu goes to rescue Inori when she becomes threatened by GHQ Endlave mechs.
Upon deciding to join Funeral Parlor, Shu begins to fall in love with Inori, who bears a striking resemblance to his late sister, Mana.
In the process, Gai and his forces fall into a trap as the Anti-Bodies decimate their ranks with a "genetic resonance" broadcast that once again unleashes the Virus throughout Tokyo.
Amidst the chaos, the leader of the Anti-Bodies, Shūichirō Keido, seizes control of GHQ and directs his attention towards wiping out the remains of Funeral Parlor.
This sudden change in fortune proves only temporary when Yu, a mysterious boy possessing the "Power of the King", appears out of thin air and kidnaps Inori, causing the outbreak to resume with full force.
Keido explains Inori was created to provide a physical body for Mana's soul so she could give birth to a new human race once the present population was destroyed by the Apocalypse Virus.
Shu's repressed memories suddenly return, causing him to remember how Mana was the first to be infected by the virus, and her mental breakdown resulted in the events of Lost Christmas.
Shu also recalls from his past that Gai is none other than Triton, a childhood friend he first met ten years ago when Mana rescued him from the sea.
Two weeks later, the GHQ under Keido's leadership seals off the area surrounding Roppongi, now called Loop 7, before proceeding to systematically eliminate the inhabitants within.
A large number of teenagers take refuge at Tennouzu High School along with Funeral Parlor members Shu, Inori, Ayase and Tsugumi.
After Gai broadcasts a message to the world not to interfere with GHQ's actions in Japan, he proceeds to help Yu and Keido resurrect Manan in Inori's body.
It is revealed that GHQ is merely serving as a front for Da'ath, an ancient cult seeking to forcefully bring about mankind's evolution with the Apocalypse Virus.
In the series' climactic final battle, Shu manages to defeat Yu and Gai while Funeral Parlor destroys GHQ's forces.
Gai also admits that he is fully aware his actions were also wrong, and that being hated by his comrades and Shu wanting to kill him makes it fair and square.
A manga adaptation titled Guilty Crown, written by Yōsuke Miyagi and illustrated by Shion Mizuki, was serialized in Square Enix's Monthly Shōnen Gangan between the November 2011[21] and December 2013 issues.
A second manga titled Guilty Crown: Dancing Endlaves, written by Gan Sunaaku and illustrated by Ryōsuke Fukai, was serialized in ASCII Media Works' Dengeki G's Magazine between the July 2012 and May 2014 issues.
Nitroplus developed a spin-off visual novel for Windows, named Guilty Crown: Lost Christmas (ギルティクラウン ロストクリスマス, Giruti Kuraun Rosuto Kurisumasu).
[27] Aiden Foote of THEM Anime Reviews agreed with Kimlinger on the presentation and plot and added that the characters are unsympathetic with back stories that do not add depth to them.
"[28] Chris Beveridge from The Fandom Post commented "While it goes big and throws a lot at us, the end result that defines the rest of the season is one that works fantastically well for me because it introduces radical change into the series."
[30] UK Anime Network commented on the series' second half that the series "bites off more than it can chew, and at times the fervent mastication that comes from this leaves certain aspects of its narrative as something of a sloppy mess, but there's still an interesting story being told here and much of it is delivered in an enjoyable fashion thanks to a superb soundtrack, slick action set pieces, and some strong ideas that make good use of the show's cast of characters."