A rude awakening to war

When they face each other for the first time in roughly three years, the two of them are forced to fight. Kira makes his first blow when he kills Miguel Aiman, a senior officer in Athrun's unit. This is painful for Athrun to watch, as he had already lost a comrade, who was meant to take the GAT-X105 Strike, during their infiltration of Orb and in the attempt to steal a Gundam. After swearing to commander Klueze he will convince Kira to join them or kill him if he has to, Athrun tries to capture Kira and force him to come to PLANTs. Other than exasperating his own team unit (especially Yzak Jule) with his inability to fight, this also puts Kira in a tight spot. In the end, Athrun's attempt to capture Kira (under the guise of reclaiming Strike), fails and causes Yzak Jule and Dearka Elthman (the two oldest in their four-man unit) to mock Athrun's ineptitude.

Athrun tries again to convince Kira to join him when Kira breaks command to return Lacus Clyne to ZAFT. After finding Lacus's life pod and bringing her on board the Archangel, Kira connected with her since she was a Coordinator like him, and was misunderstood like him; she made him feel being a Natural or Coordinator did not matter. When she was used as a hostage, Kira was disgusted and determined to set things right. He sneaks her out with the help of a friend, who pleads with him to return afterwards. When he gets close to the ZAFT ships, Kira requests for Athrun to meet him alone. Once Athrun confirms it is really Lacus and takes his fiancée on GAT-X303 Aegis, Athrun once again pleads Kira to come with him. But Kira was torn, having promised to return and wanting to protect his friends on the Archangel, he refuses again. In a rather moving moment, they shout to each other that they will shoot the next time they meet on the battlefield, knowing the time will come all too soon...

I think when Athrun first tried to capture Kira inside Strike, he was determined to not fight Kira at all, and implored Kira to not force him to fight. When Athrun tried again to convince Kira to leave the Archangel when Kira was returning Lacus, he knew it was probably his last chance. When Kira once again refuses, Athrun accepts that he will have to seriously fight Kira one day, even though it's the last thing he wants. Throughout their later battles, Athrun fights Kira, but still not with full force, and the same can probably be said for Kira. Eventually though, the emotional scars of war catches up...