I havre that issue too .....
Anyway, you will be forced into battle against the pilot of the Mr. Haptism after this battle is over and lost and you get your upgrades. After the first conflict, you wil realize that you have battled him before and you know him, but cannot exactally recall who. After a few more clashes with your steadaly upgraded machine, you realize who it is and find that he had been experimented on and driven half crazy. This and other reasons make you join the Brotherhood because he was your oldest friend and you had thought that he had died about 20-30 years ago.
For the ship: I'll work on that.