When Towelie escapes (by getting high one day and wandering off) and randomly walks into Stan Marsh's house to give towel advice, the commander of Tynacorp steals the Okama Gamesphere from the boys, in order to lure them into bringing Towelie back to his headquarters. When the boys reach the building the commander tells them that they made Towelie as the "perfect towel" but the military had captured Towelie when he escaped and tried turning him into a weapon, and that they were the ones who took the Gamesphere. The researchers then agree with the boys to infiltrate the military base to recover the Gamesphere and Towelie's TNA, then sends them there from a helicopter.
However, at the base, the military commander reveals that Tynacorp was manufacturing towels for taking over the world and that Tynacorp took the Gamesphere, so the boys must take an encryption disk and bring them down. The researchers of Tynacorp see this through a hidden camera in Towelie's fibers and are shocked that the Towelie's self-destruction sequence didn't activate, realizing that Towelie is learning compassion. The commander then releases GS-401 to overtake the boys when they return to get their Gamesphere.
At the base, the towels clash, but GS-401 is shot by the photon rifle the boys received. The researchers and military confront each other and reveal each other's secrets, but at the same time the boys see their Gamesphere and start playing again, oblivious to what the others say. The "military" is exposed as a resistance group against Tynacorp, while Tynacorp is literally uncovered to be aliens from a dying planet who make smart towels to spy on humans. Tynacorp's commander, named Zytar, commands his colleagues to fire, and then a shootout ensues. The resistance group commander quickly take the encryption disk and uploads it, starting a sequence of explosions, causing the Tynacorp building to fall apart.
The boys are blown into another room where they hang over boiling acid trying to reach the Gamesphere on another ledge, except for Kenny who drops into the acid and dies. GS-401 comes and exploits Towelie's weakness to make him choose between getting high or the lives of the boys hanging from his legs. Ultimately, Towelie chooses both by stretching his body to smoke the blunt, relaxing enough to have Kyle reach the Gamesphere. Then, an explosion sends GS-401 down to the acid, and the boys escape the crumbling building.