Clean up Amoeboids in Pumping Station is an optional mission in the re-imagined Ratchet & Clank, taking place at the Jowai Resort on planet Pokitaru. After Ratchet and Clank destroyed the hydroharvesters, Al granted Clank a Thrusterpack, allowing them to turn the special bolt crank that would grant them access the Blarg Pumping Station.
To reach the Pumping Station, head to the right from where your ship lands to find a special bolt crank, which appears different from the others. Attach the wrench to it, and with the Thrusterpack, you will be able to turn it, disabling the security barrier that blocks the entrance to the Pumping Station. With this disabled, swim to the dark blue building with an entrance in the water that has a green light over it and teleport to the Pumping Station.
Inside here, you will find the area flooded. Swim in the puddle and head to the right to find a level above with an amoeboid and a faucet for your Hydrodisplacer. Defeat the amoeboid and connect the Hydrodisplacer to drain the water. As you head down through here, you will find an Invinco-Lock to the door proceeding inwards. Unlock it with the Trespasser, kill the sharkigator here, then head back to the Hydrodisplacer plug and fill the water again. This will allow you to swim back and reach the upper level, signified by amoeboid slime.
Up here, you will find a large group of amoeboids and a special bolt crank in the middle. Defeat the amoeboids, using weapons such as the Pixelizer or Proton Drum to knock them back, then turn the bolt crank. This will trigger moving platforms placed along the left wall in the room. Climb up the platforms to reach the top of the room, where another Invinco-Lock awaits. Upon opening it, you will be led to a large, flooded area, with several explosive and metal crates. Carefully set off a few explosive crates to collect bolts and clear your path forward, but make sure not to stay underwater too long.
Eventually, swimming through will lead to another area full of amoeboids. Jump up and fight the amoeboids here, then you will reach another bolt crank. Turn it to deactivate the forcefield beside you, and you will find an O2 Mask.
Before leaving the planet, the mission "Find a way to the top of the waterfall" can still be completed here. With the O2 Mask, you can also swim in the waters around the resort to collect sunken treasure and more easily obtain gold bolts here.