Act I
Claude, the nominal leader of the "tribe", sits center stage as the tribe mingles with the audience. Tribe members Sheila, a New York University student who is a determined political activist, and Berger, an irreverent free spirit, cut a lock of Claude's hair and burn it in a receptacle. After the tribe converges in slow-motion toward the stage, through the audience, they begin their celebration as children of the Age of Aquarius ("Aquarius"). Berger removes his trousers to reveal a loincloth. Interacting with the audience, he introduces himself as a "psychedelic teddy bear" and reveals that he is "looking for my Donna" ("Donna").

The tribe recites a list of pharmaceuticals, legal and illegal ("Hashish"). Woof, a gentle soul, extols several sexual practices ("Sodomy") and says, "I grow things." He loves plants, his family and the audience, telling the audience, "We are all one." Hud, a militant African-American, is carried in upside down on a pole. He declares himself "president of the United States of Love" ("Colored Spade"). In a fake English accent, Claude says that he is "the most beautiful beast in the forest" from "Manchester, England". A tribe member reminds him that he's really from Flushing, New York ("Manchester England"). Hud, Woof and Berger declare what color they are ("I'm Black"), while Claude says that he's "invisible". The tribe recites a list of things they lack ("Ain't Got No"). Four African-American tribe members recite street signs in symbolic sequence ("Dead End").

Sheila is carried onstage ("I Believe in Love") and leads the tribe in a protest chant. Jeanie, an eccentric young woman, appears wearing a gas mask, satirizing pollution ("Air"). She is pregnant and in love with Claude. Although she wishes it was Claude's baby, she was "knocked up by some crazy speed freak". The tribe link together LBJ (President Lyndon B. Johnson), FBI (the Federal Bureau of Investigation), CIA (the Central Intelligence Agency) and LSD ("Initials"). Six members of the tribe appear dressed as Claude's parents, berating him for his various transgressions – he does not have a job, and he collects "mountains of paper" clippings and notes. They say that they will not give him any more money, and "the army'll make a man out of you", presenting him with his draft notice. In defiance, Claude leads the tribe in celebrating their vitality ("I Got Life").

After handing out imaginary pills to the tribe members, saying the pills are for high-profile people such as Richard Nixon, the Pope, and "Alabama Wallace", Berger relates how he was expelled from high school. Three tribe members dress up as principals in Hitler mustaches and swastika arm bands, mocking the American education system. Berger and the tribe defy them, singing "Going Down". Claude returns from his draft board physical, which he passed. He pretends to burn his Vietnam War draft card, which Berger reveals as a library card. Claude agonizes about what to do about being drafted.

Two tribe members dressed as tourists come down the aisle to ask the tribe why they have such long hair. In answer, Claude and Berger lead the tribe in explaining the significance of their locks ("Hair"). The woman states that kids should "be free, no guilt" and should "do whatever you want, just so long as you don't hurt anyone." She observes that long hair is natural, like the "elegant plumage" of male birds ("My Conviction"). She opens her coat to reveal that she's a man in drag. As the couple leaves, the tribe calls her Margaret Mead.

Sheila gives Berger a yellow shirt. He goofs around and ends up tearing it in two. Sheila voices her distress that Berger seems to care more about the "bleeding crowd" than about her ("Easy to Be Hard"). Jeanie summarizes everyone's romantic entanglements: "I'm hung up on Claude, Sheila's hung up on Berger, Berger is hung up everywhere. Claude is hung up on a cross over Sheila and Berger." Berger, Woof and another tribe member pay satiric tribute to the American flag as they fold it ("Don't Put it Down"). The tribe runs out to the audience, inviting them to a Be-In. After young and innocent Crissy describes "Frank Mills", a boy she's looking for, the tribe participates in the "Be-In". The men of the tribe burn their draft cards. Claude puts his card in the fire, then changes his mind and pulls it out. He asks, "where is the something, where is the someone, that tells me why I live and die?" ("Where Do I Go"). The tribe emerges naked, intoning "beads, flowers, freedom, happiness."

Act II
Four tribe members have the "Electric Blues". After a black-out, the tribe enters worshiping in an attempt to summon Claude ("Oh Great God of Power"). Claude returns from the induction center, and tribe members act out an imagined conversation from Claude's draft interview, with Hud saying "the draft is white people sending black people to make war on the yellow people to defend the land they stole from the red people". Claude gives Woof a Mick Jagger poster, and Woof is excited about the gift, as he has said he's hung up on Jagger. Three white women of the tribe tell why they like "Black Boys" ("black boys are delicious ..."), and three black women of the tribe, dressed like The Supremes, explain why they like "White Boys" ("white boys are so pretty ...").

Berger gives a joint to Claude that is laced with a hallucinogen. Claude starts to trip as the tribe acts out his visions ("Walking in Space"). He hallucinates that he is skydiving from a plane into the jungles of Vietnam. Berger appears as General George Washington and is told to retreat because of an Indian attack. The Indians shoot all of Washington's men. General Ulysses S. Grant appears and begins a roll call: Abraham Lincoln (played by a black female tribe member), John Wilkes Booth, Calvin Coolidge, Clark Gable, Scarlett O'Hara, Aretha Franklin, Colonel George Custer. Claude Bukowski is called in the roll call, but Clark Gable says "he couldn't make it". They all dance a minuet until three African witch doctors kill them – all except for Abraham Lincoln who says, "I'm one of you". Lincoln, after the three Africans sing his praises, recites an alternate version of the Gettysburg Address ("Abie Baby"). Booth shoots Lincoln, but Lincoln says to him, "I ain't dying for no white man".

As the visions continue, four Buddhist monks enter. One monk pours a can of gasoline over another monk, who is set afire (reminiscent of the self-immolation of Thích Quảng Đức) and runs off screaming. Three Catholic nuns strangle the three remaining Buddhist monks. Three astronauts shoot the nuns with ray guns. Three Chinese people stab the astronauts with knives. Three Native Americans kill the Chinese with bows and tomahawks. Three green berets kill the Native Americans with machine guns and then kill each other. A Sergeant and two parents appear holding up a suit on a hanger. The parents talk to the suit as if it is their son and they are very proud of him. The bodies rise and play like children. The play escalates to violence until they are all dead again. They rise again and comment about the casualties in Vietnam: "It's a dirty little war" ("Three-Five-Zero-Zero"). At the end of the trip sequence, two tribe members sing, over the dead bodies, a melody set to a Shakespeare speech about the nobility of Man ("What A Piece of Work Is Man").

After the trip, Claude says "I can't take this moment to moment living on the streets. ... I know what I want to be ... invisible". As they "look at the moon," Sheila and the others enjoy a light moment ("Good Morning Starshine"). The tribe pays tribute to an old mattress ("The Bed"). Claude is left alone with his doubts. He leaves as the tribe enters wrapped in blankets in the midst of a snow storm. They start a protest chant and then wonder where Claude has gone. Berger calls out "Claude! Claude!" Claude enters dressed in a military uniform, his hair short, but they do not see him because he is an invisible spirit. Claude says, "like it or not, they got me."

Claude and everyone sing "Flesh Failures". The tribe moves in front of Claude as Sheila and Dionne take up the lyric. The whole tribe launches into "Let the Sun Shine In", and as they exit, they reveal Claude lying down center stage on a black cloth. During the curtain call, the tribe reprises "Let the Sun Shine In" and brings audience members up on stage to dance.

(Note: This plot summary is based on the original Broadway script. The script has varied in subsequent productions.)