The thing is dane, you don't HAVE to have the gravity suit on when you fight mother brain. Like most of her upgrades, they are optional, meaning anything beyond her normal power suit can be taken off/deactivated.
The only reason you need the gravity suit is to walk smoothly through water and a small amount of damage reduction (if I remember correctly). As mentioned by plas durock, the mother brain fight doesn't even utilize the gravity suit damage mechanics, only the varia suit one, meaning that those who preferred the varia suit over the gravity suit could easily turn it off when they were out of the water.





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