Many years ago, Subject E-057 woke up and heard girl's voice calling for him. He followed the voice and found Marie Parfacy, a young girl who could not see or move and could only speak through telepathy. Marie asked him for his name, and when he replied that he doesn't remember anything before arriving at the super soldier project, she named him Allelujah, after what you say when you give thanks to God.
On Ptolemy, Marina asks Celestial Being to take her back to Azadistan: the country is on the brink of economic collapse due to not being part of the Federation, and has been on the brink of another civil war ever since Rasa passed away. While returning to Azadistan puts Marina at risk of being arrested by the A-Laws again, she believes that she needs to go back to save her country. Setsuna agrees to take Marina back to Azadistan. Lockon finishes a combat simulation and finds Feldt waiting for him. Lockon asks Feldt why she's been acting so oddly around him. When Haro tells Lockon about Feldt's crush on his brother, he kisses her, causing her to slap him and run away, exactly as Lyle intended.
Goodman is displeased with Kati's failure to stop Celestial Being from rescuing Allelujah and so places Major Aber Rindt, a notorious mop-up operation specialist in command of stopping Celestial Being. Rindt has already predicted a good spot to ambush Celestial Being and Goodman authorizes him to use the underwater mobile armor Trilobite as well as Mister Bushido. Kati reviews Celestial Being's tactics at the prison and thinks about how these tactics feel somewhat familiar. Louise receives orders to go to Earth with the rest the Zinin squad.
Klaus decides to help Celestial Being against the A-Laws ambush to begin an alliance between their organizations and so that Shirin can reunite with her best friend. Shirin remembers how she left Marina's service to join Katharon because she realized that Azadistan could never prosper under Federation law and asks Klaus to let her go on this mission. Back on Ptolemy, Marina asks Sestuna to return with her to Azadistan so they can rebuild the country together. Setsuna refuses because he only knows how to fight. When Marina tells Setsuna that makes her sad, he explains that he used to agree with her that fighting is inherently evil, but now he understands that sometimes, violence is the only way to defeat the distortion in the world.
Ian has Saji help him with maintanance on Ptolemy. Saji asks Ian why he joined Celestial Being. Ian explains that he wants to end war because he's seen too many battlefields. He tells Saji that everyone in Celestial Being has a similar story of being harmed by war. Allelujah has some drinks with Sumeragi and confides to her about Marie, Soma, and his desire to rescue Marie even if she hates him for destroying the super soldier instutitde and all of their friends within. Sumeragi tells Allelujah that she envies him for having a reason to fight: she joined Celestial Being to try to erase the sins of her past, but she is still haunted by them. So far as she is concerned, all she accomplished was killing countless innocents in service to her ego. Allelujah reassures her that she is better than she thinks.
The A-Laws ambush Ptolemy. The Trilobite fires missiles containing chemicals that can penetrate Ptolemy's GN field. Lasse has Ptolmey ascend to a level where the water pressure is low enough to launch the Gundams. However, his attempts to ascend are countered by depth charges from Aber and Kati's ship. Sumeragi arrives on the bridge and tells Lasse to keep ascending: the A-Laws will stop the depth charges soon so the Trilobite can safely finish Ptolemy off. The depth charges stop, and the Trilobite begins its final attack, leaving it wide open for the Gundam Meisters. The Meisters easily destroy the Trilobite, and rise to the surface to fight the A-Laws fleet. Setsuna goes to destroy Aber and Kati's ship, but he is stopped by Mister Bushido and his Ahead Sakigake. Allelujah is confronted by Soma in her Ahead Smultron. However, the battle is interrupted by the arrival of Katharon reinforcements. Kati orders the A-Laws to retreat.
Setsuna and Marina meet with Katharon. Marina is surprised to learn that Shirin is one of Katharon's commanders. Sumeragi officially rejoins Celestial Being. Billy meets with his uncle Homer to discuss his new assignment with the A-Laws. Homer is placing Billy in charge of the A-Laws's mobile suit development. Billy thinks to himself about how he will have his revenge against Kujo for her using his feeling for her.
- Ace Custom: Mister Bushido and Soma have custom Aheads.
- Bus Crash: Rasa passed away during the timeskip.
- He Is Not My Boyfriend: When Mileina asks if Setsuna and Marina are lovers, they both calmly reply that they are not.
- Ship Sinking: Lyle's harassment of Feldt kills any interest she had in him because of her crush on his brother.
- Smug Snake: Aber acts like a master strategist, but proves to be a useless coward when he is in a battle where he could be killed.