Breaking the Habit uses an anime-style animation, and was created by superflat influenced anime studio Studio 4°C. The band was shot performing the song and was rotoscoped. The animation style is tied closely to the animated segment from Kill Bill Vol. 1.

At the beginning of the video, a man is shown lying on a car's roof. The car has been surrounded by police tape, and a crowd is beginning to gather. Police are shown investigating the reason for the fall. The video then cuts to other characters, many shown to be depressed or frustrated with their lives. The first noteworthy character is a girl who breaks a mirror, then writes "I'm nothing" onto a sheet of paper. She then picks up a shard of broken glass, clenches it in her hand, and smears her blood on the paper.

Throughout the whole video, a wisp of smoke twists around the characters as their stories are played out, and Chester Bennington's face flashes around various scenes. Suddenly, the smoke flows into the mouth of the dead body, and video rewinds itself, revealing more about the characters and their stories. The dead body rockets upwards and lands on the roof of a tall building, where it is revealed that it was Chester who died. Once Chester lands on the roof, the entire band is shown playing, and finishes the song on the roof.

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