The first issues of Deadly Class focus on the story of teenage orphan Marcus Lopez Arguello as he transitions from living on the streets to being enrolled into a school of assassins. The academy, run by Master Lin, is composed of children of mob bosses and mass murderers, learning the same trade as their parents.
Marcus's decision to attend the school is one of the only decisions he gets to make for himself throughout the arc and history. His entire life has been composed of unfortunate events, each leaving him further ostracized from humanity. Marcus is homeless largely because his parents died in a horrible accident when he was young, leaving him in an orphanage whose headmaster required his manual labor for him to retain residence. This continued degradation of his sanity through the abuse by the hands of his roommates and guardians eventually drives him to committing a massive act of violence.
Deadly Class then follows the students in the academy and many of their eventual downfalls.