Mobile Suit Gundam Seed (2004)

Heliopolis, a so-called neutral space colony was holding a top-secret weapons research facility, producing Gundams for the Earth Alliance. ZAFT, which is composed of Coordinators (genetically modified/upgraded humans), attacks Heliopolis, stealing 4 out of the Alliance's 5 Gundams. In the battlefield, civilian Kira Yamato stumbles upon the Strike, the last remaining Gundam of the alliance, and is forced to pilot it. In the midst of battle he encounters his best friend, Athrun Zala, as one of the hijackers of the 5 Gundams, who sides with ZAFT. Being a Coordinator, he is the only one who can pilot the Gundam. But Kira is not with ZAFT, even though they're his own kind, nor the Alliance. Since the Alliance is the only place he could turn to at the time, he sides with them. He pilots the Gundam to protect his friends, and to fight his best friend, which pains both of them. It's a war between individual beliefs.