The boys are lost in the Andes Mountains where they discover the startling secret behind the attack of the giant guinea pigs. The boys now have the power to rescue their town and the rest of the world from the onslaught, but the Head of Homeland Security stands firmly in their way. Meanwhile, Randy bravely documents the destruction while trying to save his family.
The episode opens with a monologue by Craig, explaining what had happened in the the previous episode; the screen then changes back to the five boys and the pilots around the supposed rendezvous point.
The screen then phases to Colorado with Randy, Sharon, and Shelly Marsh hiding from the guinea pigs in their home, with Randy still videotaping them.
Guinea pigs are shown to be attacking all around the world. A guinea pig then crashes through the wall, and the Marsh family seek refuge in a damaged bus.
Meanwhile the pilot and co-pilot along with the five boys, figuring out their "meet at Peru" plan doesn't make any sense, decide to walk through the jungle since their plane has run out of fuel. They soon discover a giant area, filled with giant fruit and honeycombs. The two pilots are killed by bee larva; the boys then flee.
The focus shifts back to the Marsh family now seeking refugee on a Best Buy rooftop along with the Stotch family when a new type of guinea pigs dubbed "guinea bees" (guinea pigs wearing bee costumes; all the Guinea Creatures are likewise guinea pigs wearing various costumes) get to the roof, causing the people to flee into the supermarket itself. Randy begins to frantically film around the group. Suddenly the market is attacked by "guinea rabbits" and a "guinea mouse". They then flee into a storeroom.
The episode returns to Craig and the boys, as they find a temple in the jungle. Inside, they find drawings depicting a prophecy and detailing all the events that have occurred within the previous episode. They discover from this that the Peruvian flute bands were essential to keeping the guinea pigs within the jungle. Yet one day it was told that the flute bands would be captured and the guinea pigs would be free. Finally, it shows a picture of Craig repelling a guinea pig.
The screen changes back to Colorado. The townspeople are being attacked by a "guinea-saurus rex". At this time, Sharon has had enough of Randy's filming and decides it time to end it by punching out the camera.
Going through the cavern the boys discover a giant temple, with a pathway lined up. Here, Craig decides this has gone on long enough and leaves the temple as the boys follow him.
The boys then meet the head of Homeland Security at Machu Picchu. The Homeland Security head orders the guards to shoot at the boys, claiming that they too are Peruvian flute bands and must be stopped. Stan then explains that they are not a Peruvian flute band and that Craig and the bands are the only forces which could stop the guinea pigs.
Then director of Homeland Security snaps, revealing his plan to everyone. One of the guards shoots him in the back, causing him to reveal his true form, that of a "guinea pirate". Craig simply steps away from the scene as he does not want to interfere. He accidentally steps on a stone tile, which activates. Craig then begins to shoot energy rays from his eyes and towards the guinea pig pirate, paralyzing the guinea pirate completely.
The episode ends with a second monologue by Craig, telling the aftermath of the incident as a pan flute cover of Gary Numan's "Cars" plays in the background. The pan flute bands were released, and drove the guinea pigs away back to the jungle. While commenting on the survivors, Randy is seen once more trying to show his videos, only to realize then that he never put in tape to record the video in the first place. Craig concludes that while you never know what life has in store for you, he also states that no matter what, he would never trust the gang. The boys then come to Craig's door looking like a Mariachi band, presumably to ask Craig to invest again, but he turns them away.
Meanwhile back at the office of Homeland Security, the new Director of Homeland Security is informed that the guinea pirate has broken out of jail and has begun to attack the city. The ending sequence shows the escaped giant guinea pig roaming through the streets in his black-and-white prison uniform.