Unable to convince Kermit and his friends of the aliens' existence, Gonzo is lured by Agent Barker to K. Edgar Singer of C.O.V.N.E.T., a top secret national security facility disguised as a cement factory, whose mission is to investigate threats of extraterrestrial attacks. Singer is aware of the aliens' attempts to communicate with Earth, and having seen Gonzo on television, believes that he is the key to convincing his superior General Luft that aliens exist. Gonzo and Rizzo are taken to C.O.V.N.E.T., where Hulk Hogan, who is working there as an agent, flushes Rizzo down a tube to the facility's rat medical research held by Dr. Tucker, alongside other Muppet rats. Unable to get answers from Gonzo about the aliens, Singer decides to have Gonzo's brain surgically removed, and has him taken to a holding cell. Meanwhile, after Miss Piggy interrogates Barker, she, Kermit, Fozzie, Pepe, and Animal go to rescue Gonzo and Rizzo from C.O.V.N.E.T., using various inventions from Bunsen and Beaker. While Gonzo is in his cell, an alien channeling his voice through a sandwich asks him where the alien ship can land, and Gonzo suggests a beach known by the name of Cape Doom, unaware that Singer's assistant Agent Rentro (Bobo the Bear) is listening. Gonzo is then taken to the surgery room, and the Muppets arrive to rescue Gonzo and Rizzo. Meanwhile, Rizzo escapes from medical research and frees Gonzo from the dissection table, while Singer and Luft witness the other rats attack the surgeon Dr. Phil Van Neuter. Luft feels that his time has been wasted and angrily leaves. Upon discovering from Rentro that Gonzo is heading for Cape Doom, Singer prepares the Subatomic Neutro-Destabilizer weapon to use on the aliens. Singer and Rentro then head to Cape Doom. The Muppets rescue Gonzo from the facility, then arrive at Cape Doom where a crowd of alien believers await their arrival. After an hour-long wait, the ship comes to Earth and the aliens, who all resemble Gonzo, explain that many years ago they lost him, but now welcome him back. Singer shows up and tries to kill the aliens, ultimately failing to do so (Rentro having removed the weapon's battery) and is laughed at. Gonzo considers going with his long-lost family to their home planet, but chooses to stay on Earth with the Muppets with his family's blessing. Singer is invited by the aliens to go