Underground begins with desperation as the remaining members of the Macon 7 has split apart. Boo and Moses have gone their own way, while Cato, Noah, Rosalee, and Henry make it out on their own. They find themselves running for their lives after Henry asks a White man for a handout. Noah and Cato admonish him for being so impetuous, but he tells them they have been hiding for weeks and he only did it because he was hungry. At the plantation, the Reverend arrives and talks religion with Tom. He asks him about his soul and that of his slaves. Desperate to gain his support for Senate, he entertains him as Suzanna gives birth. One of the house slaves tells them she has given birth to a boy and Tom names him Samuel, much to Ernestine’s chagrin. Up North, John and the members of the Underground work on their secret hideaway until Kyle arrives and drafts him into the Marshalls to help them round up runaways.
Noah and the others spot a group of Whites having a party own a boat. He and Cato decide to take the boat from them to get downstream faster and hopefully get some food. Rosalee is against it, feeling it is wrong to do so. Noah ignores her and with Cato and Henry he takes the boat. August finds them and holds them hostage until Rosalee manages to release the boat from the dock. They manage to disarm, but not before he grabs Rosalee and pulls her into the water with him! The two of them struggle in the water, with Noah believing she cannot swim. He tries to get a clean shot on August, but only does so when Rosalee reveals she can swim and heads back to the boat. Noah shoots August in the back and they float downstream. That night, Tom tries to come onto Ernestine, but she resists him, telling him it is not right. The Reverend spots her coming out of Tom’s office. Up North, John uses the Marshalls to locate and protect runaways. Kyle questions him about the two runaways that attacked him and Elizabeth. He lies and tells him they would never harbor runaways. The two investigate a barn and Kyle is knocked out by a runaway–a member of The Underground, Clyde. He begs for John’s help.
August finds traveling more difficult with his wound and runs into one of the White women who were on the ship. She begs him to take her with him and his son to town. On the road, they run into Indians. August speaks to them in their tongue and allow them to cut him with their spears. On the boat, Noah and the others discover there is no food, but stay their course. Rosalee looks for clothing and finds a White man hiding under the bed. Cato threatens to kill him, but he tells them the Indians at the river’s end will help them escape to the North and that he will show them to them if they keep him alive. They reluctantly agree. Later, Cato and Rosalee argue about her usefulness. She reveals she learned to swim from their master, and Cato tells her that she is the master’s daughter. At the Big House, Ernestine confesses to The Reverend’s slave that she offed Pearly Mae. She goes onto reveal she resents being a house slave and envied how Pearly Mae had time to her family.
The next morning, Noah discovers Rosalee has abandoned them and blames Cato. He also reveals he suspects he had something to do with Zeke’s death. In town, August and his son stay at a hotel. There, the woman he helped earlier comes on to him and they have sex. At the plantation, all the slaves are baptized. The Reverend calls Ernestine a Jezebel as he dips her into the water. John wakes Kyle up and appears to have been beaten himself. He tells him that Clyde got away. Kyle apologizes for ever doubting him. However, it is for nothing as a posse of Marshalls find Clyde. As Noah and the others reach the end of the river August waits there for them. He, however, is surprised by a posse of men looking to cash in on the reward of The Macon 7. He retreats when his son tells him his wife has escaped the asylum. As Noah and the others approach the posse prepares to fire on them, until they are ambushed by Indians themselves and retreat. Noah finds Rosalee is with them!