After learning that Mr. Slave is engaged to Big Gay Al, Mrs. Garrison vows to ban same-sex marriage. Garrison starts a school project involving eggs to "prove" that same sex marriages are 'wrong'. He pairs Stan Marsh and Kyle Broflovski away from each other at first, turning them into rivals.
Mrs. Garrison pairs off the kids in her class and assigns them to care for eggs as if they were babies as part of a lesson in parenting responsibility. Everyone gets a white egg from Mr. Garrison except for Token who receives a brown one and makes a shocked facial expression. Stan is worried that he will get paired with his ex-girlfriend, Wendy Testaburger, who he has not spoken to since their breakup (a reference to Wendy's smaller part since their breakup) and he still has feelings for. To his horror, however, Wendy is assigned to Kyle Brovlofski (Stan, meanwhile, is paired with Bebe Stevens). The assignments cause tension, as Stan starts to suspect Kyle of having feelings for Wendy. Meanwhile, Bebe confesses to Wendy that she is angry at Stan's indifference to their egg, causing her to speak negatively about him. Stan calls Kyle and asks him sarcastically if he is alright. Kyle comments that the project is stupid. Stan retorts, "yeah, well so is your hat", greatly offending Kyle.
Meanwhile, Mrs Garrison has been reminded of her old boyfriend, Mr. Slave, who broke up with her after she had her sex change. Singing "Love, love lost long ago, it was special then, it's over now,...", Mrs Garrison attempts to take Mr. Slave back, only to learn that Mr. Slave is planning to marry Big Gay Al, as soon as the Colorado governor legalizes such unions. Mrs. Garrison dedicates herself to doing whatever she can to prevent their union from being legalized, hoping that, being unable to marry Al, Mr. Slave will then marry her.
The governor demands a study demonstrating that gay families are unstable before agreeing to veto the marriage bill. Mrs. Garrison thus reorganizes Stan, Kyle, Wendy and Bebe into same-sex couples, hoping that Stan's poor "parenting" skills will destroy the egg and provide the results the governor needs.
In a parody of child custody battles, Wendy becomes upset because Stan and Kyle now have the egg that originally belonged to her and Kyle, which she has become emotionally attached to. The boys remain on bad terms; Stan is still suspicious about Kyle's motives with Wendy and frequently snaps at him, while Kyle is a little confused as to what's made Stan so aggressive. Eric Cartman breaks his egg and tries to ask Mrs Garrison to give him an F and his partner an A, (resulting in a C-) arguing that, since he was the sole person responsible for the breaking of the egg his partner is blameless. However, Mrs. Garrison is so bent on getting the gay marriage law vetoed, she gives him a new one with a threat to break his legs and burn down his house if he breaks it again while strangling him. She makes plans for the final egg check in front of the governor's office, and hires an assassin to destroy the egg. However, it is then revealed that Kyle, fearing Stan's ability as a parent, gave him a fake egg and saved the real egg. He tells Stan that he had no interest in Wendy. Later, Kyle asks Stan if he really thinks his hat is stupid; Stan responds that he does not. The two boys reconcile and rush to the governor's office, narrowly escaping the assassin's gunfire, and even bombs (somehow already planted in the ground). They reach the podium weary and hurt. Stan presents the egg to Mrs. Garrison in a hoarse voice before losing consciousness and fainting. The bill passes and same-sex marriage is legalized in South Park, which confuses Kyle.
The episode concludes with Mr. Slave and Big Gay Al marrying with Father Maxi officiating. Randy Marsh congratulates Stan and Kyle for what they have done for gay marriage rights, apparently ignorant of the fact that Stan and Kyle have no idea what they actually did. Wendy apologizes to Stan for doubting his ability to be a parent. To her surprise, Stan simply dismisses her, which upsets her and causes her to leave.