Despite endless research, the human mind remains a mystery to this day. Unknown to the public, there exist special individuals who are able to dive deep into the minds of people and even manipulate their memories. Gifted with this ability, Hiroki, Tsukasa, and Satoru are among those who use their power to commit crime under the orders of their leader, Katsuragi. The three step into the dangerous territory of the human mind in order to destroy their assigned targets while striving to keep their own minds and memories safe.

Modern Germany is plagued by an outbreak of Amalgams. Existing solely to wreak havoc, these cybernetic entities spawn from rotting flesh and can fuse with technology to gain new abilities. With society left in the wake of their destruction, the Xenogenesis Assault Team (XAT) is formed to suppress the threat. Alongside its primary mission to protect against the Amalgam attacks, the organization is also researching the newly discovered amalgamated humans which possess rational thought and are far deadlier than their non-sentient counterparts. Joseph Jobson is one such amalgamated human who has full control over his powers. Although successful in his line of work as a lone warrior, an unfortunate encounter with the recently-turned-Amalgam Gerd Frentzen makes him a priority target of the XAT. As he eludes the organization and seeks new allies, Joseph is transformed into the Blassreiter—a being heralded as the strongest Amalgam in existence. Now, he must fight back with his newfound powers to uncover the truth behind not only his past, but also the entire Amalgam conflict.

Having achieved miraculous victories in a series of battles against the Britannian Army, Lelouch Lamperouge has brought the Black Knights, his paramilitary organization, to a more powerful state than ever before. Nothing seems impossible for him when he utilizes his military strength, intellect, and Geass power of absolute obedience. However, obstacles in the face of the uprising never cease, putting Lelouch in a difficult predicament. Most worryingly, Suzaku Kururugi's combat prowess and the appearance of a mysterious child named V.V. threaten to put an end to Lelouch's great rebellion.

The compilation film will recap the anime's 59 episodes from seasons one to three.