The Agent is the sixth episode of the first season of Club Penguin Shutdown.
The episode begins with a flashback of the Tuba Gang Leader looking at the rest of the Tuba Gang members, all of whom died in the rumble of the Mine. He then heads to where he had tied up the Pigtailed Girl Penguin and Girl Penguin with Bow and said how Lil_Jeffy "fucked him up and they'll die without any money." In the Snow Forts, he sells the Pigtailed Girl Penguin to the RPF leader and heads off, thinking about abandoning his criminal life. In the Clothes Shop, the Tuba Gang Leader and the Girl Penguin with Bow discuss about the Pigtailed Girl Penguin, and other topics later on. It ends with the Tuba Gang Leader seeing the deceased RPF and Cove Crew members with the minecart itself missing, simply leaving after that.
Another flashback from The Girl is then shown. In the Plaza, the Pizza Parlor explodes with The Cannibal on the ground and Lil_Jeffy falling into the pothole as he was shaking his way out of the chair. This consequently starts the episode itself.
Lil_Jeffy falls into the Underground Pool, unable to comprehend due to the explosion and hitting the ground, floating into the pool until a arm picks him up, which is revealed to be from the Agent. The Agent asks Lil_Jeffy if he was part of the EPF. Although he states that there's no other member other than him, he helps Lil_Jeffy to heal and rest for a bit until Lil_Jeffy states that he's hungry. In response, the Agent gives him some puffle-os. The Agent then begins to talk about how he's trying to find a safe zone where other penguins are surviving peacefully. He says to Lil_Jeffy that they can find it and make the island a better place, in order to undo the things the EPF did before stopping and stuttering. He tries to explain about it through stutters, saying that he wasn't apart of it and that he ran away from them, being aware of the shutdown. Lil_Jeffy drops a puffle-o and tries to grab it as the Agent continues to talk about how it is his fault for running away. He begins to have a PTSD episode and freak-out, stating that so many penguins died just as Lil_Jeffy turns his back.
Lil_Jeffy notices a paper that came out of a machine and grabs it, trying to use it to grab the puffle-o. The Agent then says that he doesn't deserve a chance as while he is surviving, all the other penguins didn't stand a chance at all. The scene then shows the window with dozens of dead penguins in the water floating lifelessly. The Narrator questions what the EPF has done to kill so many penguins. In a quick response, Lil_Jeffy accidentally knocks the machine into one of the windows. The Agent sees this and says this is what he deserves before breaking the window with more machines. He then says it's time to join the dead penguins just as Lil_Jeffy tries to escape. He uses his beak to break the window open as water and dead penguins instantly enter, breaking most of the machinery. Lil_Jeffy tries to climb up the ladder but a machinery hits it, making Lil_Jeffy almost lose grip. Another machine breaks another window and more water and dead penguins enter. The Agent begins to freak out saying this is what he deserves just as Lil_Jeffy is overtaken by a group of corpses. Seeing this, the Agent snaps back to his normal state and swims to Lil_Jeffy and grabs him to swim up to the Plaza. In the Plaza, the water explodes a bit and the Agent sees the destruction of the Plaza and questions of how long he's been down in the sewers. He then says that it's now his mission to protect Lil_Jeffy and any other penguin. The Narrator ends the episode saying that Lil_Jeffy has a new ally and questions how long they'll be safe, considering Lil_Jeffy's reputation following them.
- This is the first episode to not have an onscreen death, only showing corpses instead.