You can read the datalog after beating the game, it elaborates on what happened somewhat. I know you're right, but it just looked so not what you said.
Besides, I think I figured it out (using my ultimate mgs logic). If I kill the lieutenant Almodar before he becomea a lieuetenant, I will create a time paradox and the colonel will tell me I've changed the future. He'll also force me to restart, but I'm working on that part still...
Edit: Just downloaded the lightning dlc. Fuck balls, I thought it was fight them once and get them. Easy enough fight, but it takes a while :(. Add to that capped crystarium and any cash I get going to crystals for odin, and this is just a serious case of mindless grinding. Ah well, do want lightning on mah team, she is so fine. Amodar...has a minigun, but gold chocobird is gold and has over 1k attack, plus great everything else. Tough call.