Gather Sewer Crystals is an optional mission in Up Your Arsenal taking place in the Deep Sea Hideout, Aquatos. After stealing the star map from Nefarious' office, on the way back to the Star Explorer, Ratchet and Clank jumped down a pipe in the office leading to Aquatos' sewers. On the way back, the two met the Plumber, who offered to pay 2,000 bolts for every sewer crystal obtained. Ratchet then sought to obtain the 101 sewer crystals to earn bolts, though initially, he could only access one-sixth of the area of the sewers, before returning with Gravity Boots to access the rest.
When you land in the sewers, you will immediately be taken back to an area with a submarine back to your ship, where a cutscene will commence in which you encounter the Plumber. You have already obtained two sewer crystals from fighting the king amoeboids in "Infiltrate the underwater hideout", providing an instant 4,000 bolts.
Right now, you have access to one-sixth of the total area of the sewers, meaning you can obtain all the sewer crystals when you return later with the Gravity Boots. However, even without the Gravity Boots, you have access to 20 crystals in total, meaning you can obtain an additional 40,000 bolts, making it very worthwhile doing now.
Throughout the sewers, you will fight amoeboids in winding tunnels. The sewer crystals themselves are contained both in small containers on the ground, or found after a king amoeboid is defeated. Several weapons are useful here. The N60 Storm and Suck Cannon are useful against king amoeboids as it is single-target and also useful in an enclosed space as it will ricochet around. The Miniturret Glove and Agents of Doom is also useful to lay down several miniturrets that will take care of both the amoeboids and the king amoeboids, while the Plasma Whip can cut through waves of amoeboids before defeating the king amoeboids. In general, all weapons are useful here, and this area provides a good opportunity to upgrade them. Near the middle, you will come to rooms filled with ammo crates and nanotech, which will sustain you to keep hunting for crystals.
As you travel through the sewers, check your map using to see how much of the area you have covered. When the entire area is filled in, and you have obtained 20 sewer crystals, you can leave the planet to return later.
The sewers can be returned to after "Save Blackwater City", as the Gravity Boots are rewarded for completing Operation: BLACK TIDE. You can then return at any point when you are in need of bolts for more powerful weapons. It is good to return after completing Operation: URBAN STORM in Metropolis, as the Rangers will provide the Map-o-Matic for completing it, revealing the locations of all sewer crystals.
The amoeboids are mostly unchanged, aside from new king amoeboids which deal slightly more damage. The Qwack-O-Ray is a particularly effective weapon, as it uses no ammo, can deal with all amoeboids near-instantly, and when upgraded can almost fight your battles for you. The Bouncer and Plasma Coil are also very effective against all the enemies due to them being useful in enclosed spaces, so it may be a good idea to complete the mission when returning to visit Slim Cognito's and pick up the weapons as they go on sale, despite them being grossly overpowered.