Eyes of Skull Has A Secret is the fifth and final episode of Version 1. A malfunctioning Mega64 threatens to kill Rocko and Derek, while Sean starts to doubt his self-worth.
Sean is sitting at a table, speaking to a mysterious black figure in a sharp suit at an unknown location. The figure's body is completely hidden by his hood, mask and gloves. His voice is eerie and distorted. Sean complains about the way people treat him to the black figure. The figure makes vague comments about fate, but Sean does not understand. The figure stands up, slaps Sean in the face, and tells him "Don't be gay."
Sean hears someone calling his name, and then wakes up in Rocko and Derek's room, sitting next to the Mega64. The person he heard calling his name was Rocko. He tells Rocko and Derrick about the dream he had and asks them if they think he is cool. Derek tells Sean that he is not cool, and Rocko tells Sean to get out of the way.
Sean stands in the back of the room while Rocko contacts Poque in his apartment to find out the day's agenda. Poque is too busy arguing with Horatio about his copy of Surf Ninjas to answer at first, but stops to lay out the video games Rocko and Derek are going to be experimenting on.
While listening to the four of them talk, Sean becomes distraught. He withdraws behind the Mega64 with solitary music being played. Later, when Rocko and Derek are about to begin their first experiment, Sean enters and tries to prove he's fun by throwing a surprise pizza party. Sean inadvertently spills soda on the Mega64 while Rocko and Derek are connected, which causes it to malfunction. Poque gets angry at Sean and tells him to leave.
Due to the malfunction, Rocko and Derek are trapped in the Mega64 while their brains are frying. Poque is worried at first, but when he notices the effect this is having on their brains he decides to sacrifice them for the sake of science. Horatio is so disgusted by this, that he yells at Poque and runs out.
The insides of Derek's and Rocko's minds are shown. It is a mess of their own memories, and the Mega64's own programming, and an advertisement for Aggressive Caroling.
Back in his own room, Horatio is still bitter about Poque's callous attitude to toward Rocko and Derrick. He hacks into Poque's files, and finds the core of the Mega64. He guesses that the Mega64 can be reset by destroying the core, and calls Sean to ask for help. Sean hears Horatio's message, but ignores him and sulks off.
More imagery from Rocko and Derek's mind is shown, including a public service announcement about rabies.
Meanwhile in Poque's underground lair, Sean is still feeling sorry for himself, when Marcus appears. Marcus tries to cheer Sean up by offering him a hug, but Sean still says he feels worthless. After hearing an other one of Horatio's calls to Sean for help, Marcus gives a heartfelt speech to Sean about being different. Sean thanks Marcus, and starts feel better about himself. Seeing his job is done, Marcus leaves.
Sean hears someone else approaching, and is surprised to find that it is the mysterious black guy in a suit from his dreams. Without speaking, he hands Sean a golden helmet. Sean puts it on and loads Zelda.
Back in Poque's apartment, the power cuts out. When the backup power kicks in Poque's computer detects a new energy signal in the Mega64, more powerful than anything else that had ever been detected. Inside the Mega64, Sean suits up as Link. He sees a vision of the black figure, who tells him, "You know what you must do." And Sean runs off to destroy the core.
Watching from his room, Horatio cheers for Sean. Marcus appears and joins Horatio. Poque also sees that Sean is inside the Mega64, and is trying to destroy the core, remarking that he'll never find it. Comic relief in the form of tourists visiting the core of the Mega64 appears, and Poque says "Man, I suck."
Meanwhile more scenes from Rocko's and Derek's minds are shown, whose memories and personalities are slowly being absorbed by the Mega64's own programming. Also, Frogger.
Sean finds the core, and lifts his sword, but before he can destroy it, he is shot from behind by Poque, who has entered the Mega64 personally to take care of Sean. Sean tries to fight back, but Poque easily defeats him. Poque mocks him, but Sean refuses to give up. Powered by the strength of his heart, the master sword shoots an energy beam at the core. The core overloads, and Rocko and Derek find themselves in a strange room, the same room Sean saw in his dream of the black figure. Poque is also transported there. He exclaims "You weren't supposed to find out about this place!" Rocko and Derek attack him, but Poque holds them off long enough to reset the system to escape.
Rocko and Derek are released from the Mega64. They try to go back in to get Poque, but the system does not respond. Rocko figures out that Poque must be connected to the Mega64 somehow. Meanwhile, still trapped in the Mega64 and slowly dying from his wounds. Sean wonders off into the sunset.
Time passes. Rocko and Derek are back to normal. Sean is nowhere to be found. Poque has left his apartment to meet with two mysterious figures. They make sure he came alone and then chastise him for failing to complete his experiments, and find a distributor for the Mega64. Poque explains that he has "had to deal with viruses, robots, hackers, and a guy with a tacky yellow shirt." The mysterious figures don't care about his excuses. Poque says the mistakes will not happen again, and the figures threaten to replace him if he does not improve his performance claiming: "The rise of Mega64 is nigh, regardless." Walking away, Poque vows to continue his experiments on Rocko and Derek.
Poque is interrupted by the Sombrero Guy, who begins to narrate the epilogue. Poque yells at the man, insults his hat, and the two of them walk away in separate directions. Thus ends Version 1.
- The room that Shawn dreams of talking to The Specter in and the room where Rocko and Derek find Poque inside of the Mega64, is eventually revealed to be part of the Down community.