This is a super fun idea for a metroidvania style of game. A pleasure to experience this in a game jam!
I appreciate the fact that you're forced to use each upgrade soon after acquiring them. The swimming felt like an afterthought, though. The other upgrades got used again near the end but the swimming didn't and it was mechanically no different from climbing. Something else in its place would really add a lot to this game. Maybe some kind of breakable block upgrade which is used again during the boss battle, as one example.
The dark tunnels were a great idea and fantastic use of the "switching bodies" mechanic. But maybe a little too dark. It felt at times like I could barely even see myself, let alone where I was going. Making the available light a little more would still force you to rely on the scientist without just being frustrating.
The boss was executed really well, too! Maybe a tiny bit on the side of too fast but no real complaints about it besides that.
I am thoroughly impressed with making a game in this genre for the jam. Great job!