Meanwhile, it is learned that Richard Dawkins was the founder of worldwide atheism. Mrs. Garrison, whom he eventually married, maintained that "Logic and reason aren't enough: You also have to be a dick to everyone who doesn't think like you." As a result, atheism split into three factions. The three groups differ on what they perceive to be the answer to the "Great Question," each believing the other groups' answer to the Question is "illogical" and thus unacceptable (the AAA also objects to humans for illogically cutting down trees to make tables, instead of just eating off of their "tummies" and ironically reveres Dawkins). The Otters have set up false clam fields, which the UAA plans to attack, leaving their own city defenceless from a Unified Atheist League (UAL) attack, thus leaving both the UAA and UAL vulnerable to an attack from the AAA. When one Otter — the "Wise One" — asks if the war is truly just, and implies that perhaps it is acceptable to believe in something supernatural and/or paranormal; if only for the purpose of filling social 'needs'. After a brief reflection, he is killed by a mob of otters.
Cartman uses the Time Phone to call himself in the past, and later calls Butters and Kyle to convince both to prevent his past-self from freezing himself. He is not believed by neither his past self nor his friends, and his attempts fail. The latter call causes Kyle to miss a ride, which slightly alters certain aspects of the future (Cartman's clothes change, and his robotic dog, K-10 turns into a robotic cat called Kit-9). The massive battle between the three atheist groups begins. Cartman goes to the war room of the UAA. It is revealed that the war is being fought over "the Great Question", which is "what atheists should call themselves". Unable to reach an agreement, the atheists had split into the three now-warring factions. Kit-9 then tells Eric to call Ms. Garrison with the Time Phone. Dawkins answers while the two are having sex, and through his conversation with Cartman discovers that Ms. Garrison had a sex-change. Before which he used to be a man. Dawkins is disgusted and disturbed over the fact he had sex with a transsexual and immediately leaves. Mrs. Garrison calls him an "atheist faggot" and reverts to her old ways.
With the split between Garrison and Dawkins, the future world is altered once again. Cartman suddenly finds himself in a room with members of all three factions and Kit-9 has become Kok-A-3. In this new version of the future, the three groups are not at war with each other, having gotten rid not of religion per se, but of "all their --isms." Cartman asks if this means that there is no more war, and a sea otter answers, "Of course there's war! The stupid French-Chinese think they have a right to Hawaii!" The leaders reveal that Cartman's purpose has been fulfilled (though neither Cartman nor the viewer learn what that purpose was) and he is returned to his own time. He is told as he departs to remember that no single answer is the answer to everything.
Cartman is transported back in front of the EV Games and merges with his past self. He is initially overjoyed to be back. His mother appears and tells him that he needs to be patient, which Cartman accepts. However, he soon realizes that the future inhabitants sent him back too far, to September, changing his initial waiting time of three weeks to two months. Angry and distraught once again, he is told by an EV Games employee that there is a call for him. He answers and on the line is another future Cartman, pleading with him to not to do what he is thinking (implying he freezes himself once again). The alternate future shows future Cartman and the bald people, who were either UAL or UAA, standing or sitting on giant purple bubbles. Cartman assumes it to be a prank call from Kyle, showing that he learned absolutely nothing during his extensive ordeal in the future.