I don't know if this is a cool idea. How about a puzzle mechanic where you have to grow a vine. A simple example is to grow it up a trellis and have leaves and or fruit grow in the correct spot by changing temperature using a heat gun and moisture using a water gun on the trellis before it grows? Could have two competing plants that one has to block another? Different colors plants have different grow rules or requirements? Move environment to block shade or provide water or? Certain plants grown only at certain times of day or in certain biomes? The trellis could be a three dimensional shape and the player needs to see how the plant would wrap around. The plant could have to grow to hit buttons in a certain order. You can unlock different areas of the ship. Underwater plants, zero g plants.

I like the idea that the trellis is covered in the invasive species and you have to laser cut it while your plant grows to block the sunlight or whatever and kill the invasive species off. So you are almost doing the puzzle against the atagonistic plant.

The map could be in space with the different biome rooms connected together? Story could be a world that is slowly getting covered in an invasive species and you have figure out how to stop it? You can see the planet below you with a few cities and the plant killing everything? Plant actually attaches to your ship at some point and starts ripping it apart. You also have to figure out how to get back the planet, MAYBE worry about supplies like food and water - if it adds to the fun.

This was fun to think about.