Find Nefarious' Office and Return to the Phoenix are missions in Up Your Arsenal, taking place in the Deep Sea Hideout, Aquatos. With the help of Skid McMarx, Ratchet and Clank infiltrated the underwater hideout and met Slim Cognito, who scared off Skid. The two then took a submarine to Dr. Nefarious' underwater base, where, per Captain Qwark's plan, they split up: Clank went to the ventilation shaft with Skrunch, while Ratchet used the Tyhrra-Guise to fool the one-eyed tyhrranoids guarding Nefarious' base to let him through.
"Find Nefarious' Office" is the only mission in which you can access Nefarious' base.
First Clank section
The mission begins with Clank, who has a more limited moveset than Ratchet. Clank can jump once with , hold to glide in midair, and punch with . Head forward, jumping over the lasers, and avoid the sentinel bot's flashlight, as it will kill you instantly with a turret after it spots you. Avoid the flashlight and hit the switch in the middle to temporarily lower the force field at the end. Get past the lasers, and you will meet Skrunch and obtain the BGAMD, which fires bananas using . Hold to aim it, and fire the banana at the switch on the opposite end.
Up ahead is a sentinel bot which blocks the way forward. To get past it, fire a banana at the flashlight and have Skrunch distract it. Continue forward to a balcony at the end, where a cutscene will commence and put you in control of Ratchet.
First Ratchet section
The first Ratchet section opens with a force field guarded by a one-eyed tyhrranoid. Walk over to the tyhrranoid and press to begin dialogue with them. The dialogue is a rhythm game, in which you have to press the buttons that appear on screen as they appear to pass. Note that if you exit your disguise at any time, the defenses will instantly kill you. Complete the conversation, and then head forward, jumping across the platforms, and then initiate dialogue with the next tyhrranoid. As before, press the buttons that appear on screen, though when a button appears in a long bar, hold the button down for the length of the bar. You will need to complete two conversations to be allowed past.
After this, you will meet a tyhrranoid guarding the girder below. Complete a conversation with them to raise it to create a bridge for Clank to use, after which the gameplay returns to him.
Second Clank section
Cross the bridge and jump over the lasers to find another bridge, with a forcefield blocking your path. Fire a banana on the switch, then head to the other side of the forcefield while Skrunch has deactivated it, then stand on the next switch and fire a banana nearby to get you and Skrunch across safely. After this, head down the corridor on the right to pick up gadgebots, small robots that Clank can command by holding and selecting a command. In this case, head back to the main hallway before and select the "Attack" command to send the gadgebots to destroy the bladed spinning top blocking your path; this will destroy the gadgebot that does so, so go back to the previous room and select "Follow" for them to all follow you.
Behind this is another stationary sentinel bot. Use Skrunch to distract it, then head forward, dodging the next sentinel bot, and command the gadgebots to destroy the second spinning top. Head forward to the last room, in which you need to get gadgebots onto an elevator and use Skrunch to press a switch. Command the gadgebots to follow you onto the elevator, then fire a banana at the switch. As the elevator reaches the top, command the gadgebots to "Enter", deactivating the force field, and head forward to complete the segment. The gameplay then returns to Ratchet.
Second Ratchet section
Head forward and dodge the lasers around the switch, then run forward to get past the force field. Talk to the next tyhrranoid to open the corresponding force field. This leads to a room with no path across, until you speak to another tyhrranoid. After two conversations, a bridge will be extended across. Press the switch you come to next and head forward to finish the mission.
Afterwards you can use a sewer pipe to exit, and emerge in the sewers, where you meet the Plumber, who will give you the side mission "Gather Sewer Crystals". You can choose to gather crystals for a while, or simply return to the Starship Phoenix where you will be given the next mission, "Rendezvous on Tyhrranosis", on the next planet.