The official music video is part of the Young Blood Chronicles, a musical film produced by the group featuring each song from the album. The story continues with Stump tied in a chapel, Hurley in a room with headphones on, forced to listen to horrible music, Wentz in a room with a women taking pictures of him, and Trohman on a stage with kids throwing rotten food at him. Wentz escapes by seducing his way out. He then takes a woman's hook off her hand to kill her while the others are tortured by their captors. During his escape attempt, he rescues rapper Big Sean. When Wentz passes Stump, he puts the hook on Stump's arm stump. Wentz is quickly recaptured shortly after. Stump is electrocuted, although he is implied to have become "evil" after his procedure. With Big Sean watching nearby, the four band members are then brought to the van.
The band has played the single on The Today Show on July 19, 2013 and used the first verse as a lead on to "My Songs Know..." during an America's Got Talent guest appearance. On October 10, 2013, Fall Out Boy performed "Alone Together" on American talk show The Ellen DeGeneres Show. They also played the song during the fifth season finale of the Australian reality singing competition The X Factor on October 28, 2013 after their Save Rock and Roll Australian tour. Following the X Factor performance, the single debuted at number 40 on the Australian ARIA Singles Chart—the band's 11th entry on the chart—while Save Rock and Roll re-entered the albums chart at number 25. On November 19, Fall Out Boy was televised on Jimmy Kimmel Live! for the second time that year and played "Alone Together" and "My Songs Know..." (the latter for the second time on the show). During the 2013 Macy's Thanksgiving Day Parade, the band performed "Alone Together" on the Teenage Mutant Ninja Turtles float, with the Turtles dancing along and gesturing when the crowd was to "say yeah" as directed in the song.