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The song is the first piece to a trilogy of songs in what Vedder later described as a "mini-opera" entitled Mamasan.[4] It is composed of the songs "Alive", "Once", and "Footsteps".[4] "Alive" tells the story of a young man discovering that the man he thought was his father is actually his stepfather, while his mother’s grief leads to an incestuous relationship with the son, who strongly resembles the biological father.[4] This leads to "Once" in which the man descends into madness and goes on a killing spree, and "Footsteps" in which the man is eventually looking back from a prison cell awaiting his execution.[4]

"Alive" has been revealed by Vedder to be part autobiographical and part fiction.[4] When Vedder was a teenager, his mother revealed to him that the man he thought was his father was actually his stepfather, and that his biological father was dead.[4] The first and last verses detail those actual events, but the second verse is storytelling on Vedder's part. The lyrics of the second verse read, "Oh, she walks slowly, across a young man's room/She said I'm ready...for you/I can't remember anything to this very day/'Cept the look, the look.../Oh, you know where, now I can't see, I just stare...," and Vedder revealed that "she" was the mother, and "the look" referred to was not the look on her face, but "the look is between her legs. Where do you go with that? That's where you came from."[4]