The film follows Jonathan Shale (Tom Berenger), a highly skilled mercenary who returns to Miami after a failed mission in Cuba. He reconnects with his girlfriend, Jane Hetzko (Diane Venora), a teacher at a troubled high school plagued by gang violence and drug activity. When Jane is attacked by gang members led by the school’s feared gang leader, Juan Lacas (Marc Anthony), Shale decides to go undercover as a substitute teacher to protect her and uncover the school’s corruption.
Posing as “Mr. Smith,” Shale quickly realizes the school is controlled by fear and intimidation, with students and teachers alike at the mercy of the gang. Using his military training, he begins to clean up the classroom and win over the students, but his real target is Lacas and the drug operation running through the school.
As Shale digs deeper, he discovers that the school’s principal, Claude Rolle (Ernie Hudson), is complicit in the drug trade, working alongside Lacas. With the help of his mercenary team, Shale devises a plan to dismantle the operation and bring the criminals to justice.
The film culminates in an explosive showdown as Shale and his team confront Lacas and his gang. Using a combination of brute force and strategy, they expose the corruption and restore order to the school. The Substitute ends with Shale walking away, having brought justice to the community while reaffirming his values and loyalty to those he cares about.