Gathering Hall
Proceed out of the Save Station to the Gathering Hall. Directly to your left is a ledge. Jump up on it, turn to your right and begin working your way up the room along the ledges around the perimeter of the room. Various hazards will present themselves. Proceed to the Energy Core (Path: East Atrium, Energy Core Access, Energy Core)
Energy Core
Scan: Stone Toad
Upon entering the Energy Core there is a toxic pool ahead, and a tunnel to both left and right. Take the left tunnel, get the Stone Toad scan and roll through the Morph Ball tube.
Burn Dome
Face the miniboss, Incinerator Drone; destroy it and you'll get the Morph Ball Bomb.
Incinerator Drone
This is actually a two party miniboss: the first party is the Incinerator Drone. It shoots fire in opposite direction from its location in the center of the room. Occasionally it pops up an electric eye which is its weak point. The second party is a massive War Wasp Hive (there's no way you can get rid of it with mere missiles).
Avoid the drone's fire by focusing on the center and circling in sync with it. When the eye pops up, refocus and fire; there are two eyes that face opposite directions and only the eye itself is vulnerable. Once wounded, the drone sends a blast of fire directly at the hive, damaging the hive, and sending out angry War Wasps. Now you have wasps to fight and a blowtorch to avoid. Wash, rinse, repeat. Eventually you'll finish off the drone (4 rounds of eye pop ups), and coincidentally, the hive will be destroyed at the same time. All that's left is to collect your Morph Ball Bomb upgrade.
Don't forget to use your new upgrade to blow a hole in the Morph Ball tube, and roll through for an easy Missile Tank upgrade. Exit back to the Energy Core.
Energy Core
Defeat the Stone Toad and solve the puzzle to access the door you saw across the toxic pool when you first entered the Energy Core.
The puzzle has three triggers, the first two on timers that will expire and reset if the next trigger is not activated before the timer expires. Each trigger is the same, Morph Ball Bomb Jump into an indent just big enough to fit in, then lay a bomb in the indent. The first trigger will drain the toxic pool, the second trigger will activate the first set of platforms, the third trigger will activate the second set of platforms, allowing you access to the door that leads to the Furnace.
Furnace
The majority of the room is not accessible at this time (Spider Ball required); but a quick roll through the Morph Ball tube, and you will pick up an easy Energy Tank upgrade. Then exit back through the Energy Core to the Gathering Hall.
Watery Hall
Now that you have the Morph Ball Bomb, be sure to swing back into the Watery Hall. There is a Morph Ball tube blocked by sandstone that you can now blow through; located on the same platform that you picked up your Charged Beam from. Roll through the tube and break the grating (with a missile shot), and pick up another easy Missile Tank upgrade.