#not even getting into whether or not the real spider died defending X from preons in chapter 1 and then redips used that familiarity to

[datapilled]

I think the reason Command Mission's ending is so bittersweet, and the ending song is so melancholic, is because X couldn't save Epsilon and his cadres, along with all the other reploids that die during the story. As the story went on and it became clear that Epsilon wasn't truely maverick, especially after the first Scarface fight, X probably felt guilty but still accepted taking down Epsilon as the right thing as their actions could've triggered hundreds if not thousands or more reploids to go maverick...

And then it turns out it was a set up all along. The friend he made and lost had only been using him and his strength to get the Supra-force metal and then went entirely maverick. Despite how angry he is in game, X was probably torn up inside by Redips' reveal even when finally killing him. Then, right after Ferham showed that she wanted to do good and help, she jumps off the platform with the rest of the metal so she can die with it. He runs up to try and grab her but it's too late. She caused them so much hassle and yet he still tried to save her once he realised what she was doing.

Even if it is a different timeline, so it's not that exact same X - he probably does want a world where people don't have to die in war. He doesn't want to kill people that can still atone for their crimes. Sure, he made many allies during the game but that doesn't take away from the fact that he couldn't save all of them. And that guilt is represented with the credits song having such a melancholic mood to it.