When you reach Plankton's lair with the stolen TV remote, dodge his attacks and run clockwise (staying on the outside) around the edge of the room to pick up the Plankton Traps before they run out. When you hear the whistle indicating the traps are gone, Plankton will start following you. Dodge his attacks until he stops and looks around, then hit him with an attack and run to get 3-4 traps so you can get to the second phase a little faster. Repeat the process until he drops his shield.
In the second phase, dodge his energy blasts and pick up the Plankton traps (there will only be three this time). He won't chase you when you pick them up. As before, dodge his attacks and attack when he stops to search for you.
He'll go down and you'll get the remote back! Go back the way you came and exit to save the day.