From Fiery Airdock, head back to Gel Refinery Site. Melt the ice blocking the Morph Ball tunnels and head towards the orange door (scan it as well - each new door type is a log entry), which leads back to Imperial Hall. There's a missile expansion in here, accessed by yanking pieces of the wall down. Now head back to Main Lift, melt the ice covering the mouth piece and pass through. Solve the simple golem-bashes-the-wall puzzle and proceed through the teleporter.
Now you're in an icy cave with music reminiscent of the first Metroid Prime (nice touch). Melt any ice you see and keep moving through the breaking ice flats until you're face to face with the Screw Attack. Leap across the gap into Tower, then back up across Hall of Remembrance into the rotating hand. Look at the golem and you'll see another ship missile upgrade - grab it, then make your way back to the teleport pad. There's a Spider Ball track here too, in Tower, but you'll have to come back for it. You'll soon receive new coordinates for the G.F.S. Valhalla. You can leave and visit now if you like, but at the moment it's not all that useful. Better to stay on target and assemble the bomb on Elysia. Head back to Landing Site A, which leads to Skytram West.
This new area is overrun with space pirates. Head into the Concourse to find yet another collection of nuclear material - but you still can't move it. Navigate the surround hallways and take the elevator (behind the breakable glass) up. Keep moving along, through Chozo Observatory (which you'll definitely revist) until you reach Turbine Chamber. Fry the cords and continue on towards SkyTown Federation Landing Site, where you'll finally obtain the Ship Grapple Beam. Head back to the Observatory, call your ship to pick up the big block. Repair the broken circuit, have your ship drop the block back. Then use the bomb slot on the wall to activate the holographic projector. This lovely device will launch satellites that display item locations for the other areas, plus full maps of the planets. Come back with the Spider Ball to really clean up.
Use the Screw Attack to grab missiles in Botanica, then begin assembling the bomb. The pieces are in Turbine Chamber, Concourse and Transit Hub. You'll need the Seeker Missiles (Xenoresearch B) to grab them all, which we'll lead you to in the video as well:
Just follow the video and you should be good. It's a long process that involves Metroids, new power-ups and a couple of lengthy battles. After collecting the last piece at the Transit Hub, take the completed bomb to Spire Dock. The Aurora unit will call you back again (can't we do this over the com link?) and tell you to fly the entire dock over the Leviathan seed and drop the bomb right on top of it. So, let's.
Once you're in place, a deluge of pirate forces will descend upon your precious bomb. Defend the dock by concentrating on the enemy ships, not so much the troops. After they're gone, shut down the engines, repair your escape pod and head back to Escape Pod Bay. New mission? Fly to the seed and beat up this guy:
Helios is mostly invulnerable unless his mechanical innards are exposed. He also has several attack forms, all of which are annoying and lengthy. The basic idea to shoot him until he changes patterns, then shoot some more, the use the Hyper Beam once his weak point is revealed. As long as you scan each form, it should be no trouble taking him down - just be sure to soak up all the supplies the swarm bots leave behind after you blast their energy buildups.
Shoot the core, then off to the next mission - the pirate homeworld.