After a recap of part 1 Martin calls MOM to tell her that the good news is they've caught two of the aliens but the bad news is that number three has fled with Billy. When he tells her the aliens kept calling Billy,
Ganthar she calls them back to the Center for a briefing. MOM tells them that Billy was once known as Ganthar but in those days he was the leader of an army of alien pirates and the strongest and most savage of the renegade aliens. Under his leadership his army's mothership attacked and stripped dozens of planets of all their resources and left behind lifeless husks. But eventually Ganthar got sick of a life of unending destruction and abandoned his army and went looking for a new purpose. He crashlanded on Earth causing both the Roswell incident and the Area 51 coverup. With The Center's help Ganthar crafted a new identity for himself as the timid and tiny Billy, the complete opposite of his old self. The remaining alien contacts MOM and offers to trade Billy for his two partners and MOM agrees and assigns Martin, Diana and Java to make the trade. Martin doesn't trust the alien and wants to organize a commando raid to free Billy but MOM thinks it's too risky. Martin swipes a vial of freezing fluid off MOM's desk since they discovered in part 1 the aliens are vulnerable to cold. The spaceship touches down in New Mexico and Billy warns Martin not to make the trade because all 3 aliens are needed to call in the mothership and destroy Earth. The alien hits Billy so Martin throws the vial but the alien is ready and repels it with a forcefield so it's Martin, Java and Diana who get frozen in place. The alien frees his buddies and all 3 board the spaceship and take off with Billy. Onboard the 3 aliens merge into a single being and activate the homing beacon (they also needed to steal radioactive material to power it which was why the thefts in part 1) to call in the mothership. Ignoring MOM's order to return Martin tracks Billy to Egypt and drives there with Diana and Java. The spaceship has touched down near a pyramid and after dodging scorpions the trio think they've found him but it's the merged alien using Billy's form which separates into the three aliens and overpowers them. Locked in a storeroom with Billy they learn that the invaders are on the way and soon they'll be close enough that they won't need a beacon anymore. Seeing no alternative Billy changes back to Ganthar and breaks free and heads for the control room. The aliens have merged but they're no match for Ganthar who destroys them and the beacon. Unfortunately Ganthar seems on the verge of losing control and attacking Diana until Martin looks out the window and sees that it's too late. The Mothership is overhead and blasting everything as it clears a landing site. Ganthar takes the ship's shuttle and loads it with fuel canisters and evades the mothership's weapons as he flies into its interior. The mothership explodes from the inside and is destroyed so Earth is saved but there's no sign that Ganthar survived the blast. Back at the Center Billy's birthday party has become a wake as everyone remembers the little guy until a very singed Billy appears and says he's glad the pilot's ejection seat worked. Everyone's glad to see the little guy again and MOM gives him a special birthday present, a chip that'll prevent him ever reverting to Ganthar. Diana suggests she give Martin a chip that'll stop him acting goofy then reconsiders and says no chip's that powerful. Everyone laughs as Martin seethes with anger.