Bassist Tim Commerford claims that the song is about an old man waiting for death, who sits in a house alone after all his friends and family have passed on, waiting to be reunited with them. However, while Commerford originally thought it was a song about love and romance, band's singer-songwriter Chris Cornell explains that "It's a song about concentrating on the afterlife you would hope for, rather than the normal monotheistic approach: You work really hard all your life to be a good person and a moral persona and fair and generous, and then you go to hell anyway."
The melancholy and certain parts of the lyrics of "Like a Stone" has prompted some to wonder if Cornell wrote the song about late Alice in Chains singer Layne Staley, who died in April 2002. Cornell has denied this, saying "No. I'm not one of those guys where, like, something happens and then I go run around, 'Ooh, 9/11, and now it's 9/12, let me write about that. I wrote the lyrics before he died. [...] You can misinterpret that stuff pretty easy, but I don't tend to sit down and plan on writing about a specific issue. They come up or they don't."
The music video for "Like a Stone" was written and directed by Grammy winner Meiert Avis, who has also directed videos for State Radio, U2, Bruce Springsteen, Bob Dylan, J-Lo and many others. The video was produced by Oualid Mouaness, edited by Jim Rhoads and set in an old Spanish mansion in Los Angeles where Jimi Hendrix once lived and wrote. Commerford's then 1-year-old son was featured in the video.