Metroid Prime 2: Echoes/Power Bomb

Torvus Bog
The next upgrade is in Torvus, but it's near areas you've already been to so there's not really any new exploration involved.

Main Hydrochamber
Get to the underwater part of Torvus and go to the Main Hydrochamber; this is where you fought the Alpha Blogg. Go through the doorway opposite where you picked up the Gravity Boost, then Spider up the track to a portal.

Undertemple (Dark side)
Drop down and enter the main part of the room to start a boss battle.

Spider up to the top of the structure and grab the Power Bomb. These clear Yellow doors and destroy Benzium, and there are lots of both scattered around the game. The main problem with them is keeping topped up ammo; you only get two to start and the game is pretty stingy about dropping refills.

Blast open the Yellow door near where you picked up the Power Bomb to get out of the room.

Undertemple Access
You can either get back to the Light side via the portal here, or continue back to the Undertemple Shaft.