Tony Kushner really busts the seams with his epic Angels in America. It just doesn't fit at all into the classic plot analysis. Part of the issue is that it's hard to analyze Perestroika separately from Millennium Approaches. Another issue is that Kushner seems to be a fan of non-traditional storylines. Still, we'll try to fill in some details where they're relevant.
The initial situation for our main characters – Prior, Louis, Joe, and Harper – picks up right where it left off in Millennium Approaches. Prior is alone, recovering from his encounter with an angel that wants him to be a prophet. Harper is alone, in her imaginary world of Antarctica. Louis and Joe are together, having started a relationship.
We have multiple storylines going on here, so that means we also have several conflicts. One conflict is that Louis feels really guilty about abandoning Prior. Joe is cluing into that and feeling more vulnerable about his new relationship with Louis, especially when Louis can't seem to accept that Joe is Mormon.
Meanwhile, the angel wants Prior to be a prophet whose message is for humanity to stop growing and changing. Prior isn't really sure that he wants the job.
Harper is having a conflict of her own. She's feeling totally alone, missing Joe desperately.
The complication seems to involve Joe and Louis' relationship being on the rocks (Louis is feeling guilty about leaving Prior, and is later horrified to learn of Joe's association with Roy), and Joe and Louis' separate halfhearted attempts to get back with their former lovers.
Prior feels horribly hurt when he finds out that Louis has already moved on to another man. He stalks Joe, and then collapses in the Mormon Visitors Center. Hannah kindly brings him to the hospital. Louis' guilt is growing more intense. He visits Prior, but Prior thinks Louis isn't feeling bad enough. Though Louis says he's bruised on the inside, Prior thinks he could use a few on the outside as well.
Joe tries to return to his wife, and though they have sex, it's really no use. Joe keeps his eyes closed the whole time. He simply doesn't love Harper.
Louis and Joe's relationship explodes. Louis's guilt over abandoning Prior is really eating him up and he tries to atone. He does this in two ways: 1) picking a fight with Joe about Roy Cohn and getting beat up (just like Prior said he needed to be); 2) taking the AZT from Roy's room to give to Prior.
Meanwhile, the pesky angel visits Prior once again. He wrestles with the angel and gains access to Heaven.
Now that Louis and Joe have broken up, will the old couples reunite?
On a separate note, what's going to happen with Prior in Heaven? Will he become a prophet after all?
In Heaven, Prior confronts the angels and returns the sacred book, making them see that human beings can't simply stop moving around.
In the relationships storyline, Joe returns to Harper, but she slaps him across the face and finally ditches him, heading for San Francisco. In a similar vein, Prior tells Louis that he can never come back.
The Epilogue serves as the conclusion to the play. We don't hear anything about Joe, and are left to assume that he is all alone. The last we heard of Harper, she was flying off to San Francisco, finally gaining her own independence. The other important characters (Prior, Louis, Hannah, Belize) have managed to form a new friendship and move forward in their lives, even if Prior and Louis are no longer romantically involved.
We get the feeling that Prior still thinks he made the right decision in rejecting the angel's call to be a prophet. Though life is tough, we get the impression that Prior and the other characters feel the world is progressing.