Every ship is different. You start with one, but every time you kill a boss for the first time, you get a new one, that's just a little bit better. Use this to your advantage when fighting more difficult enemies.
Every game you play will start on the first boss. Once it dies, you move on to the next, and that goes on until you beat the latest boss that has been added to the game. Where the difficulty comes in is when you get hit, at all, as then you will die and have to restart your journey at the very first boss. Don't worry too much, however, because you will always keep any ships you got, so the first few bosses will get easier every time you fight them.
4 GB RAM
Nvidia 980 or equivalent
1 GB available space
Dude, you could probably run this on a GBA.