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.
Chykka - Larva
One of the game designers must have spent too much time at Sea World because the previous main boss, Amorbis, acted like a porpoise, and now this one acts like a whale. Start by getting a scan of it as it swims around the little island you're standing on. Every so often it will stir up some Dark Shredders from the water and these will attack. Be sure to get a scan of them too, then shoot them with Missiles to take out several at once; you'll usually get the ammo back as drops. Considering that you'll be getting ammo and health refills from them, the Shredders are actually helpful if you handle them right, so we'll concentrate on Chykka.
The larva isn't actually that hard to beat; you just need to keep your health up by defeating Shredders as they appear and avoid taking too much damage from Chykka in the first place. The main problem is that the battle takes a long time. (In fact you may notice this as a pattern for the remaining bosses in the game; there is a lengthy but easy part to get your hopes up, then a difficult part to dash those hopes and force you to repeat first part before you can try again.)
For it's first type of attack, it breaches out of the water like a big humpback and splashes the poison water over your island. Try to jump over the wave and get a shot in before it sinks again. You can tell when it's about to do something like this because it will disappear from the surface and you'll see some bubbles near where it will reappear.
Chykka's second type of attack is to jump onto you island and try to draw you into it's mouth with its tongue. This will hurt if it succeeds, but you can usually get it to let go by shooting a beam weapon at it. Light and Dark beams work well, but Missiles tend to just bounce off. If you do get Chykka to let go it will be stunned for a few seconds, which gives you a chance at its weak spot, a light colored triangle on the underside of its body. Shoot it as many times as you can with either the Light or Dark Beam to do maximum damage.
If you're not doing anything else then you might as well take pot shots at Chykka's fin as it's swimming; the amount of damage you'll do this way is minimal, but every bit helps.
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.
Chykka - Adult
For this stage of the battle there are two more forms of the monster. First Chykka's normal form, a giant winged insect appears. It tends to move around and it's difficult to keep a lock on it. Get a scan of it, then just keep firing at it with your beam weapons. Which one to use depends on how you're fixed for ammo at this point. The Power beam is weak but it will hit most often. The Light beam is strong, especially if charged, but you don't want to run low on Light ammo. The Dark beam has the most effect when it hits, but Chykka will dodge most of your shots.
When you get enough hits in, Chykka is stunned and you'll see glowing spots on each of its four wings. You need to grapple over to another island to get around behind it, then quickly target the spots with your Seeker Launcher and release before Chykka has time to recover. (You can actually use any weapon but the Seeker Launcher is most effective.) That will actually do some damage and cause Chykka to change form. In the meantime, Chykka attacks by siphoning up poison water into its tail and spraying it at you. This is hard to dodge but the main thing is to stay on your island in the safe zone. When it gets bored with this will may start flying around and try to ram you into the water, but you can probably get a few shots in when it's moving.
Chykka's new form is the Dark version. It also sprays poison water at you but it also creates baby versions of itself called Chyklings. Be sure to get scans of both when you can. As with the Shredders, the Chyklings are actually a good way to get back health and ammo, so fire at them if they're around and do your best to collect the pickups. Otherwise, shoot Chykka's abdomen with the Light Beam to do as much damage as possible. Chykka is still pretty good at dodging, but the charged Light beam scattershot should be able to hit it pretty often.
Eventually Chykka will revert to its Light version again and alternate until it's defeated. On top of everything else, the islands will occasionally destabilize and sink into the water, so watch for when they start to shake and quickly grapple to another one when they do.
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.