The game is complex enough for some brilliant emergent stories. This is one of my games:
In the first few missions I have lost one of the crew members in an away mission. We were exploring some abandoned space station. We suddenly realized its abandoned because of some sort of virulent disease break out. The away team hastily pulled out, but not before on of our crew members died of the disease. The ship was down to 2 crew members and seriously undermanned. This meant that we were taking quite a beating and even an easy encounters turned out for us a challenging fight.
Despite this, the ship was surviving and progressing, but we couldn't find anyone willing to join our crew. Than a disaster struck. While battling a pirate raider, one of his missiles scored direct hit into our shield generator room, killing another of my crew. This left me with just the captain manning the entire ship alone.
Still, amazingly he was surviving, because since he was alone, I was just leaving most of the hull depressurized to fight fire and invaders. After one FTL jump I have came across a destroyed outpost. There was no enemies in sight, but the sensors picked up a life signature onboard, and a quite lot of fire. By this time the ship was in a bad shape and I knew I will probably not make it out alive. I decided to board the outpost and try to locate some survivors. I have found one Engi alive, but on the way back tot he ship, the captain was engulfed by flames and died on the spot. The ship was crewless, and I was expecting end game.
But amazingly the Engi, after witnessing the heroic death of the lonely captain, decided to continue his quest to aid the federation. He could have just took the ship and flown away. Since he was an engi, he was excellent in repairing the ship and was actually better at running it than my old captain. Moreover since I was passing through Engi space, there was a lot of helpful allies and my Engi was receiving a lot of help and support. In a short time the ship was massively upgraded, repaired, refueled and equipped with brand new weapon systems. I had so much stuff to spare, that I could afford to help out stranded ships and stations under attack. All the while the ship was running on a single crew member - Engi that my late captain rescued at the cost of his own life.
He made it quite a journey, but sadly, recklessly jumped straight into an Ion storm and with most onboard systems knocked offline the ship was destroyed by a rebel scout.