Dark Torvus Bog
Time to face the final boss for this area and get the last upgrade. There is a final key to pick up, and just as in Agon, it's near where the battle will take place.
Get to the Dark side of Torvus Bog via either Meditation Vista or Forgotten Bridge, then make your way to Venomous Pond. As you come in from the Brooding Ground, you should be able to spot the key on a high ledge to the right. To reach it, find the Morph Ball tunnel to the left as you came in and follow it to a ledge opposite the key, then use the Grapple Beam to swing over and get it.
If you're relatively flush on ammo then get to Save Station 1 and save your progress. If your ammo is low then get to the Ammo Station under the temple to get a refill, then come back and save. The next battle is pretty tough, so you'll want to be as prepared as possible for the save in case things go pear-shaped.
Head toward the Temple.
Dark Torvus Temple
Step into the glowing orange circle to activate the keys. Poison water will start flooding the room and lift the platform you're standing on into the main part of the room. There is nothing here but a lot more poison water and some kind of giant cocoon stuck to the wall. Shoot the glowing dots on the supports to make the cocoon fall into the water and release the creature inside. The first part of the battle begins.
When the larva is defeated, the island you're on splits into three pieces and floating platforms appear with Grapple points. A second cocoon on the wall breaks open to reveal the Chykka's second form. At this point you might want to pause the game an catch your breath because the first form was just the warm up.
When the second battle is over, what's left of the poison water is drained leaving behind the dead Chykka and plenty of health and ammo pickups. Collect the Dark Visor the monster left behind and platforms rise up out of the ground and turn invisible. Switch to the Dark Visor to see them again and use them to reach the exit.
The Dark Visor isn't all that useful in terms of getting items, but you'll need it to unlock some doors to reach the next area of the game. It's also very handy for fighting certain enemies which like to appear and disappear from normal vision. But there are still a few enemies, such as the Shrieker, which can avoid being seen even with the Dark Visor.
Dark Controller Access
Use the Bomb Slot to turn the gate.
Dark Torvus Energy Controller
Get the stolen energy as in the Agon version of this room, then head back.
Dark Torvus Temple (cont.)
When you return there is a lift down to the lower part of the room. You need to return to the Light side so head for Dark Forgotten Bridge and use the portal there.
Torvus Energy Controller
When you return to the Light side go to the Torvus Energy Controller. As with Agon, repeat the same route only in reverse. Restore the energy as in Agon. You now need to go check in with U-Mos. So head back to Temple Grounds.
Main Energy Controller
There is a second dialog where U-Mos thanks you for restoring the Torvus energy. He tells you about the next destination, a fortress where the mechanoids that once protected it from the Ing have been taken over and work for them now.
Expansions (Sky Temple Grounds)
There is an additional expansion you can get now. It's near the route you take from Torvus to the Great Temple, so you might want to get it on the way.
Use the portal in the Hall of Eyes to get to Bass Access. Blast open the Green door there; this is at the opposite end from the way to the Abandoned Base.
War Ritual Ground
Go to the main part of the room where you'll have to fight off some Hunter Ing. Switch to the Dark Visor and examine the door on the tower of Ing Worms in the middle. Target the five red spots with the Seeker Launcher, then fire to open the door and collect a Missile Expansion.