In the midst of Paris' latest holodeck installment of "The Adventures of Captain Proton," Voyager runs into a gravimetric force and stops. A layer of subspace is acting as a sandbar and disrupting the ship's warp field. When distortions appear in the holodeck, the crew believes they are random fluctuations. However, while the program runs unattended, two men claiming to be from the Fifth Dimension beam down and are questioned by Doctor Chaotica. After one of them transports back to the distortion, Chaotica vows to destroy their dimension.
When weapons fire from the holodeck creates power surges on Voyager, Paris and Tuvok investigate the Captain Proton simulation. A battle has taken place, and the scenario's robot tells them invaders from the Fifth Dimension have entered through a portal. Suddenly, photonic charges begin emanating from the distortions, and Chaotica fires back with his death ray. As Paris and Tuvok gather information from Proton's ship, they encounter one of the men from the alternate universe.
Although they explain that Planet X is only a photonic simulation with which he has intersected, Paris and Tuvok can't convince the trans-dimensional alien that Chaotica's army of evil is not reality. Paris suggests to Janeway that they help the aliens defeat Chaotica so they will leave and Voyager can resume course. Janeway will play the role of Arachnia, Queen of the Spiderpeople, and charm her way into the villain's Fortress of Doom. Once inside, she will deactivate the controls of the death ray and his lightning shields, leaving Chaotica vulnerable to Proton's "destructo beam."
Posing as the President of Earth, the Doctor convinces the alien that Captain Proton needs his help. The alien agrees to cease firing and return to his realm once Proton has defeated Chaotica. Meanwhile, Janeway's Arachnia almost has Chaotica convinced to lower his shields when he becomes suspicious, and she is forced to pull a ray-gun on him. He confines her to a containment ring and fires his death ray on Proton's approaching ship. On the bridge, Torres realizes the power surges from the holodeck are pulling Voyager deeper into subspace.
Arachnia has one weapon left — her irresistible pheromones. She uses them to lure a guard into setting her free and then kills all of Chaotica's men. Defenseless, the evil doctor must deactivate his shields, allowing Proton to score a direct hit with his destructo beam against the death ray and Chaotica. Then, the distortions close, and Voyager is realigned with normal space. Another chapter of "The Adventures of Captain Proton" comes to an end ... or does it?