Ending. HELP! (SPOILERS!)

Denzel (Marco) wasn't hypnotized because he removed the chip out of his shoulder. He was just playing along so that he could actually kill Shaw and his mother.

Liev Schreiber (Shaw) on the other hand was still in puppet mode from the time his mom activated him to kill Jon Voight and his daughter. Yes Marco bit the chip out of his shoulder, but before this happened the Manchurian doctor implanted an improved on deep into his brain (this was during the first hotel scene).

In the scene at the school/polling station Shaw and Marco meet and talk. Shaw has by now uderstood that his mother is manipulating him and when she calls and the cellphone is passed from Shaw to Marco, she opens with by saying the pharses that will activate the brainwashing (is that Marco, Ben Marco, Ben Ezechial Marco? In the original book the key was to invite the subject to play solitaire until the Queen of Spades appeared)

However, as Marco is no longer under the "spell" he consciously hears the instructions to kill the newly elected president and "miss" Shaw.

Then he and Shaw decide that Shaw will either kill his mother instead of the President or even commit homicide/suicide from remorse by letting Marco fire the weapon when he has himself and his mother in the path of the bullet. Shaw does not take up the position he should because when the shot does not come as planned his mother would be alerted.

She believes something has gone amiss but not what; no matter, the President can be killed later and so she begins to celebrate the election win and Shaw can get her close to the firing line (she would not have stepped so close unless she believed the treat had passed.

That is my take on it.

In the book it is more explicit because Marco is first programmed "correctly" then re-programmed to take out the mother (I do not today recall exactly how this takes place but it uses the solitaire routine)

In the DVD commentary, the director explained that, “No matter how hard they try to control you, there is that little part of the human spirit that can not be defeated...As much as Eleanor tries to control Raymond, there is a part of him that she can’t get to, that she can’t touch.”

Shaw isn't under hypnosis during the ending of the film. It would seem that his 'handlers' either don't realise just what he knows or how mentally unstable he's become.

With the only woman he's ever loved dead by his own hands, and the realisation he's become nothing more than a puppet, he decides the only course of action he can take is to try and 'confuse' Marcos brainwashing.

Between his reaffirming of his friendship with Marco, and purposefully messing up his stage directions, he manages to tap into Marco just enough for him to take the shot.