Infiltrate the underwater hideout
Return to your ship and travel to Aquatos. In the first room, there is an Auto-Vendor. You can now purchase the Flux Rifle. Continue out of the room onto the elevator and you will meet Shadow-Dude on the other side. Take out the slimes nearby, who will split into smaller slimes a few times, and continue through to the door. The wheels on the walls can be destroyed for additional bolts. Step on the button at the end and the door will open. Take out the slimes and the flying robots. There is a Jackpot Crate in the stack of crates in the slime, so get that and break all the boxes for extra bolts. Step on the button to open the next door.
On the other side of the pit is another flying robot with a flame thrower. Take him out from a distance and Shadow-Dude will hack the computers to restore the bridge. As you enter the next room, another flying robot will come out to attack you. Clear out the enemy and boxes before stepping on the button to open the next door. There are three more robots in this room. Be careful of the exploding crate. Once the area is clear, jump into the pool of water at the end.
Underwater, there are lots of crates, each stack containing an explosive crate. Go near the crate and touch it to active the timer, it will begin to blink. Do this for all the stacks to collect the bolts. At the other end of the pool, jump out of the water, collect the bolts and climb the ladder. At the end of the pipe, there is something blocking the exit. As you approach a larger slime enemy will break through and attack you. He will spit at you to attack, but once he is killed he will not split up into smaller enemies. Killing him will earn you your first Sewer Crystal. Behind him is another smaller slime and a floating robot. Once you clear out the enemies, step on the button at the end.
Clear them all out, then step on the button to allow Shadow-Dude through. He will extend the bridge in the next room. Once you get there, 5 flying robots and two slimes will attack you. With them all shooting at you, you'll need to clear the area quickly.
Be careful when the doors open, since all 3 doors will open, and one of them has a flame thrower floating robot. Kill the robot, set off the explosive crate, then continue to the next room. It contains a large slime, two shooting robots, and a flame thrower robot. There is now another swimming section.
Jump in, trigger all the exploding boxes, and continue north through the tunnel. Be careful of the depth charges here, as they will rise or descend to hit you, or follow you if you get close enough. Clear out the rest of the exploding crates and then swim up and out of the pool. Climb the ladder to face 4 small slimes and another robot. There is also another blockage at the end of the pipe. Once you kill them, another King Amoeboid will break through the blockage to attack you. You will get a Sewer Crystal for defeating him.
Stepping on the button will let Shadow-Dude through and open a room with two shooting Guard Robots and a flame Guard Robot. Continue onto the elevator at the end of the room and step on the button in the centre. There will be a short cutscene here where you will meet Slim Cognito (from Ratchet & Clank: Going Commando). He will sell you the Miniturret Glove and Lava Gun. This will also activate the mission Visit Slim Cognito's (optional). There is also a teleporter in this room to return to your ship.
On the other side is a submarine which will take you to Nefarious' Hideout. You will now have to Find Nefarious' Office.
Visit Slim Cognito's
You must purchase all 5 Bogon Galaxy weapons from Slim Cognito to complete this mission.
Find Nefarious' Office
You will first play as Clank. Walk past the lasers and don't get caught under the light, both will instantly kill you. You will need to step on the button to temporarily deactivate the force field ahead, Run through, avoiding the lasers, and you will activate a cutscene. Clank will also receive a banana shooting weapon.
This next section is a tutorial on how to use the Banana gun. Qwark will give you a hint about how to get across the gap. Shoot a banana across and the monkey will get across to lower the bridge. The next section has a light that you can't pass. Shoot a banana through and the monkey will distract the guns long enough for you to get through. You will now reach a gap you can't pass, and will need Ratchets help.
Once you switch characters, you will activate a checkpoint and Ratchet will be in disguise. Approach the force field for a brief tutorial on using the Tyhrra-Guise. Hit the key combination that show up to say the correct phrase. If you mess up, you can retry until you get it right. From this point on, you cannot switch out of your disguise, otherwise you will be instantly killed by the security system. Jump across the floating platforms and use the Tyhrra-Guise to open the next forcefield, and get the bridge raised for Clank. This will activate another Checkpoint.
As Clank, jump past the lasers. You will need to step on the button to deactivate the next forcefield. Once you get off, you won't be able to run fast enough to get through before the barrier comes back up. To get past this section, go closer to the force field and shoot a banana back at the button. Once the forcefield shuts down, step on the button on the other side so the monkey can rejoin you. The small path to the right contains four gadgetbots. Go near them and they will follow you around. To pass the spinning blades, have the gadgetbots attack. Take the gadgetbots onto the square area at the back, then have the monkey step on the switch to raise you and the bots up. Have them enter the gadget port. Proceed down the hall to activate another checkpoint and switch back to Ratchet.
Once again, use the monkey to decoy the light security system, and the gadgetbots to destroy the other fan.
Back as Ratchet, jump over the lasers in front of you. There will be a button surrounded by rotating lasers. You will need to step on the button, run under or jump over the moving lasers ahead, and run past the forcefield before it re-materializes. On the other side, use the Tyhrra-Guise to get through the forcefield and talk to the Tyhrranoid to have the bridge extended (you'll need to pass two codes). Stand on the button at the other end to gain access to the office. Enter the room to trigger a cutscene.
Return to the Phoenix
Back as Ratchet in normal form, you'll need to return to the ship. Take the only remaining exit and you will drop down into the sewers. The stream will take you to an area with an Auto-Vendor and The Waterworker. This will unlock the Gather Sewer Crystals (optional) mission. You can return to your ship and then travel back to the Phoenix for a cutscene and your next mission on Tyhrranosis.
Gather Sewer Crystals
As you travel through the sewers, you will find 101 Sewer Crystals. You can check your progress from the Items screen. Each one you return to The Waterworker is worth 2,000 bolts. You can only access about 1/2 of the map currently. You will need the Gravity Boots to explore the rest. An item received later during a mission on Metropolis will also help you locate all the Sewer Crystals.
Once you have the item, hunt around the sewers for all the crystals. Some of them are inside King Amoeboids who hide behind a blockage in the tunnels and must be defeated to get their cyrstal. You have to approach the blockage from the correct direction or the enemy won't spawn.