In the excellent intro movie, it said....so that is the story of how Jefferson Clay died which I take to mean where he separated the saucer section and did the bonehead manoeuvre where he charged into the ship that was blocking the waypoint.

But then it continued that....he gave up his life to save more than 1500 of his fellow officers. He was the greatest hero in the history of space warfare. A role model. A legend. He made a difference by inspiring a whole generation of young officers. But of course it wasn't until 5 years later that Clay got the chance to figure out what was really going on.

I think I'm missing something here. He died and then 5 years later he was able to figure something out. Does he get resurrected or something?

...play the game and find out?

Hehe! :-) Yeah a cryptic clue that will make sense later on :-)