Henry Shackleford, a young slave living in the Kansas territory in 1856, has a run-in with abolitionist John Brown, who mistakes him for a girl and promptly “frees” him. Believing Henry to be his good luck charm, Brown welcomes him into his ragtag army and nicknames him “Onion.” Donning a dress for the first time while dodging bullets, Onion quickly awakens to the life or death stakes in the battle over human bondage and witnesses Brown's divinely inspired violent agenda: to free the land of slavery by any means necessary.

Separated from Brown's army, Onion and fellow slave Bob leave the fight in Kansas only to cross paths with pro-slavery “red shirts” who escort them to the slave-trading town of Pikesville, Missouri. Onion is taken under the wing of Pie, a mixed-race prostitute working out of the local hotel, who instructs him in the ways of the world despite her discovering his dangerous secret. Onion soon finds himself enmeshed in a mounting slave insurrection where he learns the consequences of his own actions.

Following the battle in Pikesville, John Brown, now one of the most wanted men in America, travels north with Onion to raise funds for the abolitionist cause. They take refuge at the home of famed orator and “King of the Negroes” Frederick Douglass and his two wives. When Brown and Douglass clash over methodology, Onion discovers just how complex the fight for justice and human equality really is.

John and Onion continue their fundraising mission, this time heading to Canada on foot. After seeing true freedom for the first time and frustrated with Brown's increasingly irrational behavior, Onion demands freedom from Brown's army. But, when the legendary Harriet Tubman endorses Brown in a room full of new recruits, Onion realizes that he may be more invested in the cause and the "old man" than he thought.

Onion and new recruit John Cook head to Harper's Ferry to prepare for the arrival of John Brown and his army. However, Onion quickly struggles to perform his mission of recruiting more African-American soldiers from the area when Cook's reckless behavior threatens their exposure to suspicious neighbors. After several weeks of waiting, Brown, his army and his daughter Annie finally arrive—creating a new distraction for Onion: true love.

The plan to take control of the nation's largest armory at Harper's Ferry is finally put into action. However, a crucial mistake by Onion threatens the success of the entire operation. John Brown's army takes hostages, grabbing the attention of an angry mob and local militia. With shots firing, Onion is sent out to get reinforcements.

John Brown and his remaining army take a last stand as more federal troops descend upon Harper’s Ferry. With John Brown captured and held for public execution, Onion, truly on his own, risks his life to say his goodbyes to Brown. Series finale.