The music video for the song begins with Matt Willis playing a video game called "Stay Alive". When he loses, the video zooms out to view the band playing the song's intro in a bedroom. After Charlie Simpson starts singing, they hear an explosion-like sound outside. They look out of a window to the backyard and find their neighbour Peter, played by James Bourne's brother Chris, standing next to a Vauxhall Viva customised like the DeLorean time machine from Back to the Future. They get in the car and Peter takes them to the future. The song continues as they go through a time vortex, and arrive in the year 3000. They see lots of changes, such as various aliens, flying cars and the fact that everyone now lives under the ocean. They also see three triple-breasted women. As the song continues, the three boys look at a billboard and see themselves very much older. James and Matt react embarrassed with their future selves, but Charlie nods in appreciation and looks relatively happy with his. At the song's bridge, Busted come across a concert hall with a sign saying "Busted, Live Tonight". They sneak in, lock their older selves inside a green room and jump onto the stage, where the song continues in front of an audience. At the closing of the song, the setting switches back and forth from the concert to the bedroom from the video's intro, and ends with Busted jumping into their logo.
In 2006, Bourne permitted the Jonas Brothers to make a cover of "Year 3000". Since the Jonas Brothers mainly has a pre-teen fanbase, all the sexually suggestive lyrics were simplified - the line "and your great-great-great granddaughter is pretty fine" is changed to "doin' fine" and "Triple-breasted women swim around town, totally naked" is changed to "girls there, with round hair like Star Wars, float above the floor." Also, the line "Everybody bought our seventh album, it had outsold Michael Jackson" is changed to "it had outsold Kelly Clarkson".
After the song's release in early 2007, the song debuted at #40 on the Billboard Hot 100. "Year 3000" was the group's first single to chart and their first Top 40 hit. The song eventually peaked at #31. The group's cover was the first single they released under Hollywood Records, and it was the only song Hollywood received distribution rights to after the group was dropped from Columbia. Hollywood re-released the song on the group's next album, Jonas Brothers and "Year 3000" was the lead single.
The music video for the Jonas Brothers' cover was directed by Andrew Bennett and produced by Justin Cronkite. It begins with the band entering a decorated garage, where they take their instruments: Nick and Kevin pick guitars, and Joe first plays the keyboard, then uses a microphone. As they play the intro, Nick comes home on a bike. He starts singing while the video's story side views him noticing a flash of light next door. He goes over there, and is joined by Joe and Kevin. Their neighbour "Peter" shows them that he made a time machine. However, this one is different from the one in Busted's video. This one is Pete's sofa rather than the car. While they continue to play the song, they enter the time machine, and when in the year 3000 they are in an all-white room. There they see girls with round, pink hair instead of three triple-breasted girls in Busted's. At the bridge, the girls show the band their 7th album, and the album by Kelly Clarkson that their album outsold rather than Michael Jackson. Later, one of the girls shows Joe the city on the outside, while another shows Kevin the band's "great-great-great granddaughters". Towards the end of the song, the brothers jump into the time machine and return to their own time. At the end of the song, Nick sings, while Joe claps the rhythm and Kevin plays the ending riff on his guitar.