Tips for Gameplay
What to do during the first flashback (after opened the door and went down the stairs)
Go down the ladders all the way and approach the left-most wall. A prompt will be shown to check the wall and put C4 on it.
How to solve sensor laser puzzle and open the door
You can use the invisibility to get past laser tripwires without triggering them.
After a certain point in the game, you can find this new ability for Carrion's base (small) form that allows you to become invisible in exchange for energy (indicated by a blue bar in lower left corner of the screen). Again: you have to get this ability to get past the lasers without triggering them. If you run out of energy, you will then have to charge it by using the batteries.
How to supposed to get through the Leviathan Reef Bridge Base puzzle
You have to take control of the flame soldier for a second time and pull the lever. It took me a minute to find out you can control NPCs bodies multiple times (as long as they don't get destroyed).
How to fit through the weird blocky crate
One you break by pulling the other you have to upgrade your mass and backtrack.
Can you use multiple offensive skills at once
You don't. Even though one command is tap and one is hold, you can't have both abilities set at the same time. You'll have one offense and one defense skill at a time. You have to lose biomass to "downgrade" your ability. You can deposit it in the water and then retrieve it after you're done.