First Visit: Helping the Islanders and Mayor
Ratchet and Talwyn arrive on the planet by cannon. Ratchet gets up, and sees a mirage of Clank. He thinks that Clank is on the planet, so he begins exploration of the level. He believes that there must be some reason that he was sent to the planet. He soon learns of his wrenches new pick-up and magnetic techniques. Along the path, they meet up with Mayor Barnabus Worley, who welcomes them to the planet and explains some things. Talwyn asks if the planet has a radio tower they could make a call from, but the mayor tells them that it was vandalized last night. They can use it if they find a way to fit it, which involves cranking a few bolts on the wind turbines. They also meet with with The Smuggler, a character from Tools of Destruction, and his parrot.
Ratchet speaks with the turbine operator, who tell them that the Smuggler keeps shutting off the wind turbines for some reason, and the parrot has been stealing the towns goods. Ratchet decides to help him get the wind generators up and running again, with use of his trusty wrench, Gravity Boots (for walking up metel pathways), and Grind Boots (for grinding on rails).
After Ratchet fixes the five wind turbines, he makes his way to meet Talwyn at the Beacon area. The beacon operator tells Ratchet that The Smuggler stole a bolt it needs to work, so Ratchet and Talwyn split up to look for the bolt needed. Ratchet goes to the beach to speak with the Smuggler, who sells Ratchet the stolen bolt for 10,000 bolts. He brings it back to the beacon operator, who fixes the beacon. Ratchet cranks another bolt, and then goes up the tower to crank the last bolt. Ratchet is thanked for saving the planet, and the Mayor takes him and Talwyn to a special room on the island, containing the Obsidian Eye. Ratchet must find something to make the machine work, so the Mayor gives Ratchet a diary entry of Darkwater, giving some information on where to go next (find the Fulcrum Star and you will find Clank). The Fulcrum Star is a stabilized black hole that allows people to look across long distances in space/time.
Rusty Pete soon arrives on the planet, and tells the duo that he has found some new information on Darkwater, so they go back to the beach to meet him. He says to trust him because he wants to help, and also learn more about what is going on.
 Second Visit: Stopping the Pirate Assault
Ratchet and Talwyn return to the island, in search of Captain Slag and Rusty Pete. The Mayor says they are being attacked by Pirates, and that some of Ratchet's weapons washed up on shore recently. Darkwater's ship soon arrives, and the island is then attacked by Pirates. Ratchet and Talwyn fend them off fdor awhile with their weapons, and then Ratchet mans a turret for awhile, destroying the Pirate ships' turrets. When the turrets are destroyed, Ratchet and Talwyn then need to protect the door to the Obsidian Eye room, which is soon attacked by Pirates. After the door is safe, Ratchet must go back and use the turret to destroy a new set of turrets on the ship.
Once the turrets are destroyed, the evil Pirates leave the area. Ratchet finds a map (which is assumed to lead to Darkwater's treasure), so he brings it back to the Mayor to translate. He cannot read it, so Ratchet brings it to the Smuggler. He offers to act as a guide and take Ratchet to Darkwater's Cove (where the treasure is assumed to be) for 12,500 bolts. You do so, and soon set off.
 Third Visit: The Truth about Clank and the Zoni
The 3rd visit is just a cutscene after you defeat Captain Slag. You imput the Fulcrum Star into the Obsidian Eye machine, and then are shown where Clank is. He is in a room, surrounded by some Zoni. A door opens, and the presumed dead Dr. Nefarious (main boss from Up Your Arsenal) walks in the room and calls for Lawrence. This obviously sets up the beginning of the story for the next game, and raises so many questions in every players mind on what this means, based on past games, Quest for Booty, and the next game.
The following cutscene shows Rusty Pete closing the book he was reading the story from. He is on a floating crate in the water, rowing along with one hand and holding Slag-on-a-stick. They are on a hunt to find Slag a new body.