The Federation's peacekeeping force A-Laws attacks the anti-Federation group Katharon's asteroid base Resolas and effortlessly destroys it thanks to the A-Laws's new Aheads and GN-XIII's. When Katharon's leader Klaus Grado receives news of this attack, he tells his second-in-command Shirin Bakhtiar that he has decided to move up the date of Katharon's plan to rescue their comrades from Proud.
Colonel Sergei Smirnov, who has been living with Soma Peries as father and daughter since the fall of Celestial Being, gets a phone call from Colonel Kati Mannequin, who has been offered a position with the A-Laws and has decided to accept so she can figure out just what the A-Laws are doing.
Saji Crossroad finishes his shift as a colony engineer on board the space colony Proud. The A-Laws show up and arrest one of Saji's coworkers for conspiring with Katharon. When Saji voices his confusion, the A-Laws arrest him as well and sentence him to hard labor in a prison camp within Proud.
Katharon prepares to assault Proud to liberate the prison camp there. Admiral Arthur Goodman of the A-Laws is aware of Katharon's plans and orders Barack Zinin and his team, which includes Warrant Officer Louise Halevy, to attack. Ian Vashti and his daughter Mileina inform Tieria Erde of the A-Laws's movements. He decides to launch in Gundam Seravee, because he believes that "he" will show up. Meanwhile, Setsuna F. Seiei quietly infiltrates Proud.
Katharon attacks Proud, but the Zinin squad destroys their ship. Zinin deploys automatons into Proud, which begin to slaughter the prisoners. Saji is about to be killed, when he is saved by Setsuna. The two of them are surprised to reunited.
As Setsuna fights his way through the automatons with Saji in tow, he laments how the world hasn't changed despite everything Celestial Being sacrificed to unify it. Setsuna manages to reach the Exia Repair. Saji is horrified to learn that he was saved by a Gundam Meister.
Setsuna launches in the Exia, but it is no match for Zinin's Ahead. Louise has a panic attack upon seeing the Exia. Her eyes glow gold, allowing Ribbons Almark to see through them. The Zinin team is about to kill Setsuna when he is saved by Tieria and the Gundam Seravee. The Zinin squad is forced to retreat.
On board the Ptolemaios II, Feldt Grace, Lasse Aeon, Ian, and Mileina are overjoyed that Setsuna is back. Setsuna and Tieria's reunion is interrupted when Saji accuses Celestial Being of murdering Kinue and maiming Louise. Saji steals Setsuna's gun, but ultimately can't bring himself to fire because he doesn't want to become a killer like Setsuna. Tieria has Saji locked in Ptolemy's brig and reminds him that Setsuna wouldn't have been able to save Saji if he weren't willing to kill.
The media broadcasts the news that Celestial Being has returned. Goodman decides ot use this new crisis to expand the A-Laws's authority. Louise takes pills for her panic attacks, causing Zinin to wonder how someone so sick managed to get recruited to the A-Laws. Klaus tells Shirin that he wnat to ally with Celestial Being, as he believes that they share a common goal with Katharon. Regene Regetta tells Ribbons that he has a guest: Wang Liu Mei. Sergei receives a visit from his estranged son, A-Laws Second Lieutenant Andrei Smirnov, who has orders for Soma.
Setsuna takes a look at the new 00 Gundam before heading down to Earth. He meets with Neil Dylandy's twin brother, Lyle, who is a Katharon agent. Setsuna tells Lyle that he has come to recruit him to be the new Lockon Stratos.
- Dramatic Irony: Louise takes part in an operation that would have killed Saji. Neither of them are aware of this.
- If You Kill Him, You Will Be Just Like Him!: Saji refuses to kill Setsuna because he doesn't want to become a killer like him.
- Nice Job Breaking It, Hero: By unifiying the world, Celestial Being accidentally created a brutal dictatorship.
- So Last Season: The Exia is no match for the five-years more advanced Ahead.
- Villain Opening Scene: The season opens with the A-Laws attacking a Katharon base.
- Wham Shot: The last shot before the credits shows that Allelujah has been imprisoned.
