Infiltrate the underwater hideout is a mission in Up Your Arsenal, taking place in the Deep Sea Hideout, Aquatos. After winning the Tyhrra-Guise from Annihilation Nation, Ratchet and Clank returned to the Starship Phoenix, where Captain Qwark had drawn up a plan to infiltrate Dr. Nefarious' Deep Sea Hideout on Aquatos. Ratchet and Clank traveled to the planet, where they were backed up by Skid McMarx using the Hacker.
At the Gadgetron vendor, the Flux Rifle becomes available. This is a sniper rifle that fires powerful shots at enemies from afar. Though it becomes useful later, the weapon is generally not useful on Aquatos as there are few opportunities to snipe at enemies from a distance. Instead, it is worthwhile picking up any previously available weapons you have not already obtained, such as the Suck Cannon, Agents of Doom, and Spitting Hydra. Though the Infector has its uses in some circumstances on other planets, the enemies here already fight one another anyway.
When you arrive on Aquatos, head east to a tunnel, which will take you underground, to where the mission takes place. You will encounter Skid McMarx, and a small cutscene begins. Proceed forward and you will encounter the amoeboids. These enemies come in a variety of sizes, and the larger amoeboids will split into smaller amoeboids after being defeated. As they are found in hordes, weapons such as the Plasma Whip, Spitting Hydra, Nitro Launcher, and Shock Blaster are best for dealing with them. Defeat the amoeboids and head forward, hitting the switch to open the door, where you will encounter two hover bots, flying enemies that shoot both you and amoeboids with ranged flame attacks, or simply fire a continuous flame attack in front of them. These are tougher enemies that can sustain more damage and are more spread out, and thus, are better defeated with weapons such as the N60 Storm, Agents of Doom, or the Spitting Hydra if targeting multiple.
After defeating the hover bots, jump up on the ledge through the next door, and you will encounter a few amoeboids and hover bots. Once they are defeated, Skid will use his Hacker to extend a bridge across to the next area. Defeat the enemies, and then jump in to swim: hold to dive, hold to rise, and hold to swim faster. Touch the explosive crates to destroy nearby crates for bolts (swimming away before they explode), and eventually you will reach an exit to the pool above.
Sasha will warn you of a large biomass, and shortly after you will face a king amoeboid, a particularly tough amoeboid that can sustain a lot of damage. Defeat it with single-target, high damaging weapons such as the Agents of Doom or Suck Cannon, and then progress forward and hit a switch, allowing Skid to come through to this room and the next. Here, defeat the hover bots and Skid will use the Hacker to create a bridge across. In the next room, defeat a large group of amoeboids and hover bots, and at the end, flip a switch to create a door on the left to another pool of water.
Defeat the enemies and dive in the pool of water. This time, when swimming, make sure to avoid the mines by swimming faster than them. At the end of the pool, once again climb out and fight a king amoeboid through a tunnel, and then activate a switch at the end. Skid will use the hacker one last time after you defeat the final set of enemies. When Skid extends the bridge, use the tunnel elevator to begin a cutscene. Here, you will encounter Slim Cognito, who sells Megacorp weapons from Going Commando. At the moment, Slim only sells the Miniturret Glove and the Lava Gun, both of which are extremely useful weapons. If you have a save file of Going Commando in which you purchased them, they will be obtained for free here; otherwise, they are nonetheless worth buying.
After this, head to a submarine at the end of the base to begin a transition, leading to the next mission, "Find Nefarious' Office".