Grace is the young supervisor at Short Term 12, a group home dedicated to assisting troubled teenagers. Her life is shared with her long-term boyfriend and colleague, Mason, but she struggles to communicate her emotions to him. The revelation of her pregnancy prompts her to book an abortion appointment; she excitedly informs the elated Mason about her condition but omits her intention of terminating it.
Within the facility, Grace and Mason devote their attention to Marcus, a resident on the brink of turning 18, who grapples with the anxiety of leaving the support of the home. Grace forges a connection with Jayden, a newcomer at Short Term 12 troubled by a pattern of self-harm. Jayden tends to isolate herself from the other residents, hinting at her temporary stay, and when her father fails to pick her up on her birthday, she violently lashes out at the staff. After this episode, Grace spends time in the "cool-down room" with Jayden, revealing her own scars from past struggles.
As the birthday festivities continue that evening, Jayden decides to leave the facility without anyone knowing. Unable to compel her return, Grace follows Jayden to her father's house, only to find it deserted. After their fruitless attempt, the two head back to Short Term 12, where Jayden shares a mysterious story she penned, leading Grace to speculate that Jayden may have suffered abuse at the hands of her father.
During a gathering held by Mason's foster parents, he surprises Grace with a marriage proposal, which she happily accepts. However, the next morning brings distress when she receives a call informing her of her father's release from prison. This news deeply troubles her, creating a rift between her and Mason, who cannot comfort her as she grapples with her emotions.
Upon returning to Short Term 12, Grace learns that Jayden has been picked up by her father. This infuriates her; however, her boss insists Jayden had denied any abuse. Tragically, later that day, Marcus attempts to take his own life following the death of his pet fish.
As Grace waits at the hospital for Marcus's treatment, she experiences an emotional breakdown, which leads to a confrontation with Mason. He urges her to open up about her feelings, but she, instead, reveals her intent to abort the pregnancy and ends their engagement. In a moment of rage, Grace heads back to Jayden's father's home, considering reprisal, but Jayden interjects with the idea to vandalize his car instead.
An intimate conversation ensues between the two, where Grace unveils her own painful history of sexual abuse inflicted by her father. In response, Jayden shares the bruises she has endured from her father, prompting them to return to Short Term 12 together, where Jayden courageously reports her father for the physical abuse suffered.
Having resolved a few issues, Grace reconciles with Mason, who shares that Marcus's condition is improving. In the backdrop of her emotional healing, several weeks pass wherein Grace begins therapy and views a sonogram with Mason, showing hope for reconciliation and new beginnings.
