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The Professor asks the rest of the crew to throw away the product of his latest experiment, a two-foot-cubic yellow box, by throwing it into the sun. Under no circumstances are they to look into the box-it is absolutely forbidden. Bender and Fry steal the box during Amy’s watch, but it’s a decoy Leela planted–she still has custody of the real one. After a sleepless night of watching over the box, Leela succumbs to her curiosity and looks in, only to be sucked through to a parallel universe where there almost exact, but slightly different, versions of each of the Planet Express team.
The Professor (in parallel Universe B, "Professor B") explains that parallel universes almost always contain evil versions of each other, and sends Leela B through the Universe B blue box to see if Universe A is evil. At gunpoint, Leela B herds Fry A, Bender A, Professor A, Amy A, and Zoidberg A through the yellow box and into Universe B. Professor B hides his blue box and will only bring it out when he is convinced Universe A is not evil and will not destroy the yellow box containing Universe B. Each team member is charged with looking after their counterpart, and contrary to expectation, each pair bonds. Professors A and B call the crews back together to announce good news-none of them are evil. Hermes B walks into the room and asks why they aren’t all out destroying Professor B’s blue box, and Professor B says the box can’t be destroyed because that would be the end of his new friend, Professor A. Professor A then realizes that Hermes A must be preparing to destroy the yellow box in Universe A. Professor B goes to retrieve his box from its hiding place so they can stop Hermes A in Universe A, but the Zoidbergs have stolen the blue box and are playing with it out in the alley.
In Universe A, Hermes A heads toward the Sun to destroy the yellow box. In Universe B, Professor B decides they should to make a new box, and starts up a conveyor belt that turns out scores of identical blue boxes. However, each of the boxes has some glitch in the parallel universe it connects to-one is too cold, one is all women, etc. As the crews consider their fate, Zoidbergs A and B come in with the original blue box and in the scuffle to get it, the original blue box gets mixed in with the pile of other blue boxes. Professor B figures out that they can all look into boxes if they tie on to each other with wire so they each be pulled into the appropriate box when it is found. The crew members find a sightless universe, bobbleheaded universe, robot universe, ancient Rome universe, carnival universe, and the Professors eventually find the original box in a hippie universe. All of the crew members are pulled back into Universe A, and stop Hermes A from throwing the yellow box into the sun. The Planet Express crew members say goodbye to their parallel selves, and the Universe B members return to Universe B.