I had been annihilating - I had a great strategy which relied slightly on my 5-shot lasers, and my two-man away team: A mantis and a crystal. Together the away team was unstoppable - I'd create a 1-room stronghold and teleport away if I was in danger. They'd take down the shields for my 5-shot, or just take over the entire ship if it didn't have a large crew.
So I had been neglecting my main ship, except defenses (FTL drive & shields). I was at the seventh sector, last battle... They tried to flee. I sent the away team to attack the captain... You can't fly a ship with no bridge crew, right?
Wrong. My perfect team -- which could have easily turned the mother ship into scrap -- was kidnapped. After mourning their losses, we moved on to the final battle... And got annihilated. It would have been so easy with that away team... But alas, they're probably someone's slaves now. An ancient, lost race and a bold warrior, subject to slavery.
So I guess the federation will have to wait for its grand victory.