ZAFT units attack Orb’s Murasame forces. Meyrin helps bring Athrun to the bridge. Outside, Murrue takes Neo to the Sky Grasper. He asks what’s going on, and she tells him that if he stays he’ll be injured again. She then says that he isn’t Mu and runs away with tears on her eyes. Athrun tries to convince Meyrin to get off the ship because they’ll be fighting ZAFT, but she insists on coming. The Archangel launches from its underwater dock, and nearby Shinn launches from the Minerva in the Destiny Gundam. Shinn destroys several Murasames and is then attacked by Cagalli’s Akatsuki Gundam. On the Minerva, Talia speaks with the ZAFT field commander, and he tells her that not only have they not found Djibril, but Orb’s forces have reorganized and are putting up fierce resistance. Cagalli fires her beam rifle and cannon at Shinn, but he blocks both attacks with his beam shield. Shinn fires his beam cannon at Cagalli, but the Akatsuki Gundam’s armor reflects the shot back at him. Several Murasames arrive to back up Cagalli, but Shinn destroys them all with his anti-ship sword. He then uses one of his beam boomerangs to cut off the Akatsuki Gundam’s left forearm. He tosses another beam boomerang at the Akatsuki Gundam, but Kira descends into the atmosphere just in time to destroy the boomerang and save Cagalli. Lacus accompanies Kira in the Infinite Justice Gundam and flies away to land on the Archangel. Kira tells Cagalli to leave because he’ll handle Shinn. The Archangel pulls in near Onogoro Island and picks up the Minerva on its sensors. Both ships deploy their weapons and begin firing at each other. Shinn and Kira attack each other with their swords and beam sabers. Kira fires the Strike Freedom‘s combined beam rifles and Shinn fires his cannon, but the shots hit each other and dispel the energy.
ZAFT’s mobile suits continue to attack Orb’s mobile suit and ground defenses. Cagalli destroys a GOUF Ignited and is joined by Kisaka and several Murasames on her way to the National Defense Headquarters. A ZAFT descent pod enters the battlefield, and three DOM Troopers piloted by Hilda Harken, Mars Simeon and Herbert Von Reinhardt land and begin attacking ZAFT units. Lacus tells Murrue and Cagalli that the DOM Troopers are allies. Hilda tells Mars and Herbert to move out, and they use the Jet Stream Attack to destroy many ZAKU Warriors and GOUF Igniteds. Athrun and Meyrin go down to the mobile suit hangar, and Athrun says he’s surprised to see Lacus piloting a mobile suit. The Archangel and Minerva continue to shoot at each other and inflict minimal damage. Shinn presses his attack, and Kira goes into SEED mode and blocks Shinn’s sword with both his hands. Kira then blasts Shinn away with his rail cannons, and Shinn goes into SEED mode as well and attacks again. Rey calls Talia and says that Shinn should come back for repairs, and Talia says the either he or Lunamaria will have to go out instead. Djibril runs through a building and is escorted by several Orb soldiers. A Geo GOOhN breaks out from the ground and shoots at the National Defense Headquarters building, but Cagalli destroys it before landing. Shinn is frustrated over not being able to shoot down Kira, and Rey orders him to retreat. Elsewhere, Cagalli goes into the room where Yuna is being held captive and punches him in the face. Athrun asks Cagalli if the Infinite Justice is for him, and she says that’s for him to decide. Cagalli demands to know where Djibril is, but Yuna says he doesn’t know. She then says they’re both to blame for what happened, but even then she says she believed Yuna would’ve wanted to protect Orb. Kisaka says that they need to capture Djibril. Kira stays on the battlefield and disables ZAFT suits. Athrun asks Lacus if even she thinks he’s just a fighter. She says that even if he is, he’s still Athrun. She says that Kira wanted to give him Infinite Justice because the worst thing of all is not being able to do anything when you want to do something. The Minerva fires several missiles at the Archangel, but Neo destroys them with the Sky Grasper. He calls Murrue and says he did it because he doesn’t like the Minerva. He tells her they can win and says that he’s the man who makes the impossible possible. Shinn prepares to sortie, and when Lunamaria tries to go after him, Rey tells her she’s a hindrance to Shinn. Shinn then launches in the Destiny Gundam, followed by Rey in the Legend Gundam. As they attack Kira, Athrun launches in the Infinite Justice.
After the pointless clip show, we get back to the main story. However, nothing of any importance occurs despite this being an all-battle episode. Kira and Shinn fight each other for the first time in their new Gundams, but nothing really happens. Djibril is still on the run and has Orb soldiers helping him. Lacus brings the Infinite Justice Gundam down to Athrun and answers all his questions with non-question. Since he’s the eternal non-thinker, he’s angry and goes out to fight anyway. This episode sees the introduction of the DOM Trooper, yet another item from the Universal Century making its way into the Cosmic Era. The Jet Stream Attack is also used, but this time it actually works. Neo uses the Sky Grasper to some effect, and it’s more Mu than poor Murrue can handle. Although this episode is mostly action, there’s nothing interesting. The fighting is exactly like everything seen in previous battles. Some time also seems to be wasted with people launching everywhere. Overall, not much seems different here from the end of episode 40.