For a three-act plot analysis, put on your screenwriter’s hat. Moviemakers know the formula well: at the end of Act One, the main character is drawn in completely to a conflict. During Act Two, she is farthest away from her goals. At the end of Act Three, the story is resolved.
Act I
The main character, named "the kid," runs away from home at the age of fourteen. And boy oh boy, is life ever hard on him. After a few years of getting stabbed and shot in bars, he finds his way into an American band of mercenaries led by a nutty guy named Captain White. This band of merry men rides into Mexico with some vague plan of conquering the country and making it part of the U.S. But they're promptly wiped out by a band of Apaches and the kid makes a narrow escape only to wind up in jail.
Act II
The kid gets bailed out of jail by a man named Judge Holden, who met the kid briefly back in the States before Captain White's crew left for Mexico. Holden hires the kid and some other prisoners to join a group of men led by a dude name Glanton. These guys have a contract with the Mexican government to hunt Apaches and trade their scalps for money. It looks like the Mexicans hate the Apaches even more than they hate Americans—go figure. Glanton and his crowd ride up and down the country killing Apaches. But they quickly burn through all their good will with the Mexicans by becoming total bullies and doing whatever they want all the time, which includes firing their guns at random people when they're drunk.
Act III
Eventually, Glanton's luck runs out and his whole group gets wiped out by a bunch of angry Yumas (Aboriginal peoples). The only survivors are the kid, Judge Holden, and a few other men who end up getting hanged by the Mexican government anyway. Judge Holden tries to murder the kid for always being such a weak, compassionate fool. But the kid escapes. They don't meet again until ten years later, when the judge confronts the kid in the doorway of an outhouse and pulls him inside. The judge comes out, but the kid doesn't, which suggests that the judge has murdered the kid. In classic McCarthy-esque fashion, though, we never know one way or the other.