Why not add the ability to create a Cloner Ship or Mothership or something like that? You have to find like 5 parts in the Space Stage, and once you do, you'll gain access to a Spaceship part that you can add to your Spaceship. Once you do this, your spaceship will grow in size, be more powerful, but also be slower. The most important feature in this would be the ability to create Drones, or any other name for the sort of ships. So when you enter combat, smaller ships start pouring out of that Spaceship part I talked about earlier.
Like I said before, you'll need to collect the parts to create the Spaceship part first. Maybe they could add some kind of Parts Creator, which gives you, say, 15 pieces of scrap, including the 5 parts you collected and it will give you a picture of what a part is supposed to look like. Once you assemble the right pieces in the right place, you'll unlock that part in the Spaceship Editor.
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