After you regain Power Bombs, Adam asks you to return to your ship for important information.
Find an Alternate Route to your Ship
Ride the elevator up to the Main Deck, then take the Main Elevator up. Suddenly the power cuts out and the elevator stalls in the middle... uh oh... Shoot repeatedly to the right to open a tunnel. Roll through. Continue through the tunnel to fall through some Pit Blocks, while some eerie music plays. The Seerook in here will retract when you approach; if you stand still they will open back up again and you can kill them, but you have to hit their middles; their sides are invulnerable. If you can't kill it, just freeze it and go past. Make your way through this passage, and at the end morph into a ball and jump up against the right wall to go through a tunnel.
Suddenly you find yourself face-to-face with a frozen Ridley in sub-zero containment (whom you may have already seen if you wandered around on the Main Deck earlier). Approach it, and its eyes start to glow... uh oh. A Core-X will float out of it, and it will crumble.
Walk to the right to fall through some Pit Blocks into another dark passage. From where you fall, drop a Power Bomb to reveal a tunnel to the left, and roll through it to the end, where you should drop another Power Bomb. More pipe will be exposed, revealing a Power Bomb Tank. You'll have to stand up and jump to reach it. Go back the way you came out of this pipe, and where the enemies are lay some Power Bombs to kill them. Once they're all gone, stand at the left edge of the floor and make a running start towards the right. You'll destroy some blocks with a Speed Boost in the next room.
You seem to be at a dead end, but a Power Bomb will reveal a way out (and a Missile Tank, so get that before moving on). Jump up to the corridor above and exit right. Make your way to the Docking Bays.
Run to the right to your ship and stand below it to be pulled up into it. Your energy and weapons will be recharged, and you can save the game.
Adam informs you that the main silo of the Reactor Core has gone offline. Your destination is somewhere below you, where you can start auxiliary power. Adam then tells you the important information he brought you here for: the Etecoons and Dachoras have boarded your ship. Since they haven't been infected by the X, Adam will allow them to stay there.