They Came from Outer Space: Part 2 is the second episode of the second season of the animated series, Martin Mystery. It was originally released on October 29, 2004 and it was also the continuation of the second part of the episode.
MOM reveals Billy's hidden life as Ganthar, destroyer of worlds before he abandoned his old name, form and way of life and joined the Center. She send the gang to trade the captured aliens for Billy, unaware that once the aliens reunite they'll be able to call in reinforcements and destroy the earth! The only one who can stop them is Billy but to do that he'll have to become Ganthar again and he might not change back.
The team still can't believe that the third alien got away with Billy. Martin contacts M.O.M. about what has happened, including the fact that the aliens kept calling Billy "Ganthar". M.O.M. tells the agents to come back to the Center immediately, saying that there are things they need to know. Back at the Center, M.O.M tells the agents about Billy's secret past. It turns out Billy was used to be know as Ganthar, the leader of a very dangerous group of rouge aliens, and he was legendary for being the most savage and powerful of all the aliens. This fact put the team in shock, Diana states " Talk about not knowing someone! Billy has more skeletons in his closet than a graveyard". They went into Billy's room, M.O.M turns on a hologram of a galaxy filled of brown planets. M.O.M tells the team that these are the planets conquered by Ganthar's army; after they took the planet over, they stripped them of their resource, destroying all life in the process, then they move on to the next (the classic definition of conquer). Diana realizes the reason why the invaders are on Earth; they're going to destroy it! Martin notices that only planet is blue. M.O.M tells them that's where Billy had enough. All those years of destroying planets took a toll on him. One day, he just snuck away from his army. Diana asks how did Billy end up working for the Center. M.O.M shows them a video clip of him; he arrived on Earth in the Roswell UFO Incident in his original form. Martin is confused, because Billy is the exact opposite of Ganthar and the aliens they captured. M.O.M. tells them that's exactly what Billy wanted. When Billy joined the Protection Program, he used his shape-shifting abilities to create the Billy that everybody know. Martin wonders if Billy still has some of his old powers. M.O.M. tell them that he still has some powers, but vows never to use them; he's afraid if he does, he'll become evil once again.
They get interrupted by the alien who captured Billy, saying if they want him back, they must return his captured comrades or Billy will pay the price. Out of reluctance, M.O.M accepted the conditions. Martin, in shock, knowing that the aliens can't be trust and suggests to free Billy with a commando raid ASAP. M.O.M. objects " No, Martin! I won't risk anymore of my agents captured. We will do exactly as he says. We need Billy back safely. He's our only hope to stop the invasion!" The team meet up in desert, Martin still thinks the exchange is a bad idea. The spaceship shows up and the alien brought out Billy, tied up. Billy shouts, " Don't do the exchange! It take all three of them to operate their transmission beckon!" The alien slimes Billy to silence him. Furious, Martin forgets about the plan, and took immediate action by using the insect secretion he stole from M.O.M's office. Billy shouts out not to do it, but was too late. The alien uses a force field and used the secretion against them. He then freed his comrades and walked over to the team to finish them, but stepped on the ice, causing them to back off.
Somewhere in Egypt, the aliens tells Billy to rejoin them or perish. Billy refuse to rejoin them, they tell him that they have summoned the mother ship and there's nothing that he or his friends can do to stop it. Mourning came and the team tells M.O.M. that the exchange was a total disaster. M.O.M has worse news; a huge ship is rapidly approaching the Solar System. She says that without Billy, Earth is in serious trouble and she'll give the team a briefing. Diana scolds Martin for not sticking with plan. Martin already feel bad for letting Billy down; Diana reminds him that Billy is her friend too. Martin tries to contact Billy with the U-watch, asks him for his exact location Billy whispers the coordinates and adds "These aliens are the scouts. They set up a transmission beckon to summon the mother ship. If the mother ship lands, Earth is doomed." before the transmission got cut off. Later, Diana suggests to look for the transmission beckon. Martin insist on finding Billy first. They hear Billy's voice followed it into the Pyramid, but reveals to be a trap!
The alien scout threw the team in the prison chamber. Billy asks if they took out the transmitter. Diana says they didn't because Martin wanted recuse him first. Martin says " Blowing up the transmitter would have been a pretty good birthday present for ya, huh?" Billy is surprised that the team remembered his birthday. Diana, not wanting to ruin the moment, ask where the transmission beckon, Billy says " It's in the bridge. They use radiation to power it up to contact the mother ship. There are thousands of warriors on board, ready to set up their colony. And then they'll take the Earth's resources. Minerals, trees, water, everything!" Martin asks if Billy was really their leader. Billy admits that he did things he's not proud of, but insists that he has changed.
Martin thinks about smashing through the window, but it's completely shatter-proof. Martin notices the mother ship has almost land. Diana says that there is not way that Earth can fight it; all hope is lost. Martin suggests "Unless, Billy becomes Ganthar and uses his powers." Billy doesn't want to do it, fearing he would change, stay evil and end up like his former comrades. Which cause Billy to break down in tears, the team tells him it'll be okay and they will find another way. Billy took a deep breath and transforms in Ganthar. He breaks out the prison cell and confronts his former comrades, when the alien merged into one, he frozen them and threw them at the transmission beckon. Ganthar realizes there was not much time left, he hops into s fighter ship and head for the mother ship head on. The team watches in horror that Billy just saved the world at the cost of his life.
Back at the Center, the team and M.O.M. are still in shock about Billy being gone and saying he was a hero. Suddenly, Billy shows up, injured but okay nonetheless. Billy tells them that he aimed for the mother ship's power core and that was it. It was the only way to save the planet, he's just thankful that the eject button worked. Java asks if Billy was hurt, he say he's sore from transforming into Ganthar. M.O.M show Billy a chip they developed to make it impossible for Billy to ever change back. Billy replies, "It's a great gift, but I don't need it! I faced my dark side and I survived, I'll never change back again." The episode ends with Diana saying if they the chip to Martin, maybe he'll stop being a goof all the time. Then says, "Nope, I don't think it's powerful enough for that." causing everybody to laugh at Martin, feel irked.