Battle your way to the launch site[edit]
On your way over, the Infernox armor will be delivered to the Armor Vendor on the Phoenix. Slim Cognito will also inform you that the Shield Charger is available. All the lights on this platform can be destroyed for bolts. Approach the Hypershot targets to the west. From there you can see two Four-Eyed Tyhrranoids on the platform below. Snipe them from up here then use the Hypershot to swing down. Once you land, the door will open and inside is another Tyhrranoid. Once he's defeated, two large Tyhrranoids will start shooting from the other side of the building.
Once they're dead, advance to the other side of the room. Two large Tyhrranoids are on the other side on raised platforms. Throw down a shield and snipe them. Jump across to their platform and run up the side of the building. As you run around the hot section on the side of the building, two large Tyhrranoids will come out. Defeat them and continue up the building, jumping over the next section of hot tiles.
Once you step on the button here to deactivate the forcefield, Sasha will give you a hint to use the Tyhrra-Guise. Equip it and go up to the Tyhrranoid and have him step on the button. He will take some convincing so you'll have to complete four segments to get through. Proceed forward and destroy all the crates here for over 6,000 bolts.
Climb the ladder but stop on the first ledge and equip the Tyhrra-Guise. After four rounds of translation he'll let you pass to the elevator to his right. Ride it down and some Troopers will attack. There is a Jackpot crate here. On the other side of the gap is a Four-Eyed Tyhrranoid and two large Tyhrranoids on his sides. Use the Flux Rifle to take them out from behind the edge of the building, then collect all the bolts in the area.
When ready, activate the Hypershot platform ahead and double jump to it, and then to the ground behind it. As soon as you land, the door ahead of you will open and two large Tyhrranoids will attack. Defeat them and destroy the crates inside the room. Continue along the path and four Troopers will attack. Defeat them without going too far up the ramp.
At the top, there are two large Tyhrranoids near the front, two Four-Eyed Tyhrranoids in the back on towers, and a number of small Troopers in the area. You can take out the large enemies in the front before the enemies in the back start shooting.
You will need to use the hacker to unlock the door at the back of the room. There are two large Tyhrranoids on the ground, and one above on the left. There are a lot of crates in this room so collect all the bolts. Then switch to the Refractor. Bend the laser beam at the sensor in the center of the room which will split it into two. Turn the bolt to reorient the sensor so each of the split beams is accessible on either side of the room. Point the two lasers at the sensors in either side of the door.
Inside, there are two large Tyhrranoids and two Four-Eyed Tyhrranoids on the ground, and two Four-Eyed Tyhrranoids on towers in the back. Take out the ground enemies before entering the room since five large Tyhrranoids will enter from the back door once they're defeated. They may get stuck in the doorway, and one may get stuck in the next room. Once you enter that room, you will have a Continue Point. Break all the crates and continue through the final doors for a cinematic.
Defeat Dr. Nefarious[edit]
You will skydive out of a plane. Avoid the red missiles. When you land there will be a cutscene after which you must defeat Dr. Nefarious.
Defeat the Biobliterator[edit]
Get into the hovercraft and defeat him. If it's destroyed use the buggy to get to the hangar and pick up another.
Challenge Mode[edit]
Once defeated, you'll be able to choose to return to before you battled the boss, so you can go back and collect any missed skill points or titanium bolts. Or you can begin Challenge Mode. You will begin the game again with stronger enemies, but keep all your current weapons, armor, items, and the Charge Boots. You will lose all five Qwark vid-comics, the Refractor, the Hypershot, the Tyhrra-Guise, the Warp Pad and the Gravity Boots. You will keep all your Titanium Bolts, but you will have to find the Sewer Crystals again. Mega versions of all the weapons will be available for sale from any Auto-Vendor and the Infernox armor will be available from the Armor Vendor on the Phoenix. When attacking enemies, you will have a bolt multiplier active. The multiplier will keep increasing up to a max of 20x until you are hit, at which point it will drop back to 1x.