When he sees the judge coming, Tobin tells the kid to save himself and move on. But when the kid starts to go, Tobin heads after him.
They hide under an old wagon and wait for the judge to pass by. When the judge passes, the kid has another chance to shoot him but doesn't. Eventually, the judge gives a speech about how he knows the kid is not taking his chance to shoot. He says that the kid has always been a traitor because he has always had sympathy for the aboriginals that Glanton's band has been killing. The judge also insists that he has left Toadvine and Brown alive. In other words, he didn't kill them for their guns. We don't know if this is true, though.
With this said, the judge moves on and walks off into the desert with the wild man at his side.
As the narrator tells us, the kid and Tobin would have died if a group of aboriginals hadn't found them and nursed them back to health. Maybe that sympathy the kid was harboring for these folks was warranted after all.
Eventually, the kid and Tobin reach San Diego, where Tobin goes to find a doctor while the kid stares out at the ocean.