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Dr. Mary Cooper was a member of the Right Arm, as well as a former member of WICKED (alternatively WCKD). This character was created for The Scorch Trials film and does not appear in any of the main books.
The Scorch Trials Graphic Novel
In Scorched, Mary is working for the Right Arm, a group that is working against WCKD with the goal of stopping their plans to kidnap innocent, immune children for their tests. When Brenda asks for help, Jorge takes Brenda to Mary. Eventually, both of them discover that she is also privately testing immune children for effects to the Flare and they turn against her, refusing to help when WCKD shows up to destroy the Right Arm's camp.
World Gone Wicked
In World Gone Wicked, Mary works as a doctor for WCKD before Ava Paige joins the organization. She approves Mary's chemical to be distributed among people to wipe out some of the population, thus triggering the Flare. However, Mary never foresaw it mutating and evolving to the point where people have become Cranks. A year passes and Mary shares her speculations of the disease with Ava, suggesting that there are children immune to the effects of the disease. Ava considers that as the key for the cure to the disease and eventually starts sending in a number of immune children for testing. Seeing the amount of children brought in for testing, Mary expresses her concern about them to Ava, but she assures her by telling her she is doing the right thing for the good of the world, adding that Mary is her "right arm." Years pass and a cure seems nowhere in sight. Ava decides to remove Mary from the project when the latter begins to question her earlier intentions and work. Mary escapes, leaving a note for Ava that she is now working against her.
In Maze Runner: The Scorch Trials, Mary is part of the Right Arm and serves as their doctor and right hand to Vince. She emerges from a tent in the base to stop Vince when he tries to shoot Brenda, who has been infected by a Crank bite. She greets Thomas and observes his reaction to her, noting that "They would put you in the Maze after what you'd done." When Thomas asks her to clarify, she explains that she used to work for WCKD and that the first time they met, he told her that he couldn't take it anymore, watching his friends get sent up and killed in the Maze after so many years. This made him turn over the information for all of the WCKD labs, bases, and warehouses to her and encouraged her to leave WCKD to try to stop them, thus forming the Right Arm.
Mary instructs volunteers from the group to help carry Brenda into the medical tent and she draws blood from Thomas to construct a temporary treatment for Brenda. She explains why WCKD was taking kids – the children were born with some kind of enzyme that made them immune to The Flare, which is why WCKD wanted to study the kids in situations like the Maze to see what would happen. Thomas asks if she's found a cure but she reveals that the problem is, the cure cannot be manmade, hence why WCKD is forced to harvest Immunes for the fluids and organs to try to concoct a cure. She injects Brenda with the mixture and explains that this is a temporary fix – Brenda will always need more. She and Jorge exit the tent to give Thomas time with Brenda, but she warns Thomas that Brenda cannot come with them.
When WCKD invades the Right Arm's base, Mary is forced into a kneeling line with Vince and some of the other volunteers. She reveals herself to Ava Paige, declaring that at least she'll die with a conscience. The two speak briefly before A.D. Janson shoots her in the chest. Vince tries to stem the flow of blood but Mary dies in his arms.
In Maze Runner: The Death Cure, Mary's name was engraved on the rock along with the names of victims from the war with WCKD.