The night after Ezra's funeral, a Chantyman lies sprawled in the shadow of a dock warehouse in East Boston. A clipper ship is moored along the wharf, and the refrain of "Shenandoah" can be heard from the ship coming into harbor. The Chantyman listens critically and belts out his own version in a surprisingly good, albeit drunken, tenor. The companionway door on the clipper ship's poop deck opens, and Brant emerges cautiously. The Chantyman accidentally lurches forward, and Brant threateningly turns his revolver on him.
Brant realizes his error, and the bawdy Chantyman asks him if he might need him for his next voyage. When Brant turns him down, the Chantyman laments that "Everything is dyin'" these days, noting the deaths of Abe Lincoln and the great Ezra Mannon. Brant changes the subject and gives the Chantyman a dollar to go drinking. To Brant's dismay, the Chantyman begins to sing "Hanging Johnny" and teeters off.
Christine, dressed in black, emerges from the darkness. The lovers meet on the poop deck. Christine begins to tell Adam what has transpired; she has come because her children are out visiting friends. The two retire to the cabin to speak in private. Lavinia and an enraged Orin appear on the deck.
The scene fades to black. When the lights return, a section of the ship has been removed to reveal the interior of the cabin. A haggard Christine finishes her story while her children listen on the deck above. Brant laments his cowardice. The two decide to flee to China on a passenger ship and seek out their Blessed Islands. Fearing the hour, Christine turns to go, and the lovers painfully bid each other farewell.
The children enter the cabin. Orin moves to follow them, but Lavinia restrains him. They must do all according to plan. If they are caught, no justice would be done. Orin slips out. When Brant returns, he re-enters and shoots him with his pistol almost at Brant's body. Lavinia stares at Brant's face, and then orders Orin to make it seem that Brant has been robbed. She forces herself to wish the corpse peace.
Orin returns and strangely notes Brant's resemblance to his father. The scene is like his dream: he has killed him before, over and over. Perhaps he has even committed suicide. If he had been Brant, he would have done as he did—loved Mother and killed Father. "It's queer!" Orin exclaims. "It's a rotten dirty joke on someone!" Lavinia rushes him out.