As 1999 is ending, Cartman discovers blood coming out of his anus, leading him to believe he is experiencing his first period. He taunts the other boys for not having hit puberty yet, unaware that his bleeding is caused by a minor stomach infection that has spread across South Park, and that it can be cured with antibiotics. Kenny later contracts the same ailment, and Kyle, not wanting to be left out, pretends he is also afflicted. The boys consequently abandon Stan and refuse to play with him, believing he is less mature for not having had his period.
Meanwhile, the people of the world flock around Jesus' house, excited about the Millennium and saying that, at the year 2000, Jesus's dad should make an appearance. Jesus contacts his father and tells him about his potential resurgence in popularity, but God (unseen in their conversation) says He will not show up because mankind is not ready. Jesus, wanting to still satisfy the people, books Rod Stewart to play a New Year's Eve concert in Las Vegas; everybody decides to go, because a rumor persists that God will show up.
Stan, meanwhile, prays for his period, but does not get it, so he visits Dr. Mephisto and gets a bottle of hormone pills. Using them causes Stan to grow a beard, have a deeper voice and develop a pair of breasts, but still no "period." Afterwards, Kenny suddenly bursts from inside out. At the hospital, they discover that Kenny shoved a tampon up his ass, causing him to explode. The doctor expresses concern that "the children are all shoving tampons up their ass because they've seen the Backstreet Boys doing it on TV or something."
The crowd in Las Vegas for the New Year's concert is enraged upon seeing Rod Stewart (portrayed here as very old and incontinent) and they turn against Jesus. With them preparing to crucify him again, Stan asks Jesus why God does not answer his prayers, and Jesus explains that, if God does everything for you, then your existence has no real purpose. Jesus realizes that this was God's message: Jesus had to figure his own way to get people to follow him. And just as he realizes this, God arrives.
After the crowd's initial shock over God's appearance (distinctly unlike traditional depictions of God), God offers the people the chance to ask one question. The crowd plans to ask the meaning of life or existence, but before anyone else can ask, Stan comes up and asks why he hasn't gotten his period. God explains that boys don't get periods, and tells the truth: that Cartman and Kenny are affected by the colon infection and Kyle was lying to fit in with them. God explains to Stan that he will never get a period (because he's a man with titties), but he will hit puberty when the time is right. He then returns to Heaven, saying He will answer another question in the year 4000. Stan is satisfied by this, and joyfully starts singing "Auld Lang Syne", but the angry crowd turns on him for wasting their chance to ask a very important question to God, right at the time as the credits roll.
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