Once he convinced Nicol Alex, the people of the security company would be close by as he needed to watch out for Nicol doing something out of place before he could take Nicol to the plants, while also not having the situation of Athrun and Kira change too much. Alex had the transport plane fly towards Mentor Malchio's Island home, where he took care of the orphans, but it landed on a nearby small Island instead, as he knew the next battle would take place there. As for not going to the Malchio Island, one reason is that he didn't want to involve himself with the man, and another is that he is very doubtful of the guy's motives.
After arriving at the Island he had the Plane covered with camouflage using anti-radar material cloth. stayed in a highland where he could have a good view of the surroundings, so that he could immediately find out once the ZAFT attacks the Archangel. During the following day, Nicol asked Alex many times when he would be able to talk to his parents, to which Alex said that he would leave with Nicol to the plants once the Archangel gets into the EA air defense airspace. Alex didn't say he would leave after the next battle, as that would make many doubt his purpose in why he only intervened in these two battles and saving Nicol and Tolle. Tolle could still be explained off as not wanting to see a friend die, but the same logic could not be said for Nicol. Leaving after the battle will make many think he did intervene with the two as his specific targets, then they will wonder how he knew that they might be in danger.
But if Alex stayed till Archangel reached EA air defense, everyone would only think he was worried about his friends and temporary companions. As for the sudden intervention in Nicol's case, it can be explained as an action that happened while testing the new Custom Blitz and Custom Guul, which was exactly what he explained to the other when he brought Nicol. Nicol asked why Alex was waiting here instead of following the Archangel, if he was worried about it, to which Alex responded by saying that the Archangel would need to go through here to reach EA controlled zone, and it would only take the Archangel a day or so to reach here.
While on Archangel, Kira was alone, thinking about his actions and all that happened during his time in the Archangel, even though there was no Frey to mess with him, and he also didn't experience the inability to protect the civilians, as the shuttle was not destroyed. He still felt very conflicted about his feelings for war and thought about what was necessary so that war could end and there would be no more in the future, as he didn't want anyone to have to fight to the death and leave their loved ones grieving.
The next day, the ZAFT submarine vessel, which was tracking the Archangel, finally got the signal from it on the radar, and after noticing its path and realizing that the area with many small islands in the morning was the perfect place to ambush, it immediately had the members of the Zala team launch. Soon after the Aegis, Duel, Buster, and Rusty's DINN left the ship, followed by three Guuls for the Aegis, Duel, and Buster. As for Miguel, his DINN was damaged beyond repair in the previous battle, and there is no more MS on the ship, so he could only stay on the ship.
In the Archangel, as soon as the ZAFT ship released the MS, its radar picked up the signals, and an alert was raised, causing everyone to get to their post in haste.
Kira also launched in the Aile Striker Pack, and Mu left in the Skygrasper with Launcher Striker Pack. Kira took the Strike to the middle deck of the Archangel and, using it as a foothold to save energy, he started attacking the Aegis, Duel, and the DINN. As for the Buster on the other side, Mu attacked it with his Skygrasper.
Kira was having a hard time fighting Athrun, who was angry and attacking with all his strength, and Duel, who was charging with a determination to die together, while also handling equally troublesome attacks from DINN. But still with a very hard fight, he damaged the wings of the DINN and also destroyed the leg of the Duel when Yzak was jumping around recklessly from his Guul, which caused his MS to almost fall into the water, which was saved by Rusty, who returned to the ship with the Duel to not become a burden to the Aegis and Buster in the battle during this time Aegis destroyed 2 of the 75mm Automatic Multi-Barrel CIWS while also destroying one of the Linear cannons with his Scylla Multi Phase Beam Cannon. Athrun, who saw Yzak being shot down, attacked Kira by sending his Guul at the Strike and exploding it with a Beam Rifle when it was close to the Strike. Kira, whose Beam Rifle was destroyed when he shot down the Duel, could only watch as the Guul exploded and pushed him down towards the islands while Athrun followed in the Aegis and attacked the Strike falling towards the island as well.
On the other side, Tolle is preparing to launch out in the Skygrasper to support the Strike, but under the Busters heavy fire and the previous damage, the Archangel finally fell on the island at the same time Mu in the Skygrasper used the Agni cannon to finally destroy the Guul on which the Buster was on, while also firing to destroy the Buster but with Dearka's desperate maneuvering sacrificing the right hand the Buster evade being destroyed completely but the secondary damage from the Agni cannon and fall caused the Buster to be completely incapable of moving. As Dearka watched the Dual high energy beam cannons of Archangel being aimed at him, with no choice, he came out of the cockpit to surrender, as he didn't want to die. As for Mu Dearka's final attempt at the Skygrasper, which destroyed the unit of the Launcher Striker Pack, causing him to throw the whole unit to save his own life and return to the Archangel, because despite dumping the pack, his Skygrasper still took damage.
Back on the side of Kira and Athrun, their fight, which had entered into a melee, had become very intense with repeated clashes of the beam sabers. At this time, Alex, who had already gotten onto his Custom Blitz and the Custom Guul was already in the airspace close to the battle, also noticed Tolle coming out of the Archangel in the Skygrasper and attacking the Aegis with Missiles despite Kira's warning, and was attacked by the Aegis shield, which was thrown by Athrun. Alex, who saw this, knew that this was the most challenging and hardest part for him, as he had to rip out the cockpit of the Skygrasper while also filling it with ablation gel to keep Tolle from dying from an angle where the shield thrown by the Aegis prevents both Kira and Athrun from noticing his actions.
Alex, using all his concentration, swiftly reached for the Skygrasper. Maybe it is Tolle's luck or the high emotional stimulation Alex suddenly activated the SEED factor in his genes and got to the position where he could avoid being seen ripping out the cockpit of the Skygrasper while also ensuring that the ripped out part of the Skygrasper was also not visible to Kira and Athrun. With the SEED factor's absolute control and ability to use the whole body and brain's reaction speed, Alex was able to rip out the cockpit while also using the Ablation Gel to save Tolle from the heat of both the claw and the explosion damage of the Skygrasper.
Kira, who watched what he thought was Tolle's murder, was instantly overwhelmed with shock and anger. Seeing Athrun Zala destroy Tolle's Skygrasper, who was attempting to protect him, shattered Kira's composure. He cried out in agony and was immediately thrown into a deep, uncontrolled rage. This intense emotional trauma (grief over Nicol's death earlier, coupled with rage over Tolle's) caused Kira to trigger the SEED factor in a state of pure, emotional carnage, rather than focused skill. His immediate response was not tactical; he engaged in single combat with Athrun's Aegis Gundam with the singular, rage-fueled intention of destroying his friend, completely disregarding his own safety.
And Athrun, who was also fighting Kira with rage over Nicol's death and with the thought of destroying Kira even at the cost of his life, also triggered the SEED factor and fought desperately with the will to die together. With both attacking each other without any rational thought, they fought a battle of injury for injury until Athrun finally caught Kira in the MA weapon form, trying to destroy Kira with the Scylla Beam cannon, only to find his battery empty and his PS armor going down, so Athrun activated the Aegis's self-destruct to kill Kira while he got out of the cockpit.