The story revolves around a war between the Earth Alliance and ZAFT (Zodiac Allied of Freedom Treaty) treaty. Ages ago a man altered his genes to bring out his full genetic potential. He became the first coordinator.
He announced this in the hopes of inspiring others to strive to be the best. What he did was create a conflict between coordinators and naturals (normal born unaltered humans).
The story centers around Kira Yamato a coordinator who is dragged into the war by fate. He witnesses the attack on his home colony and the abduction of four of the five Earth Mobile Suits (later dubbed Gundams).
During the abduction he comes face to face with one of the thieves, Athrun Zala, his childhood friend.
Throughout the anime Kira has many doubts and uncertainties because of his nature and the fact that he's fighting against his own kind while striving to protect his friends. (Incomplete)