Dr. M is the main antagonist in Sly 3: Honor Among Thieves, who serves as the final boss in addition to the crux of the plot. He operates on Kaine Island where the Cooper Vault is located and is obsessed with cracking it. Wanting to reclaim his family's legacy and treasure, Sly expands the Cooper Gang to include new members.
The mandrill had once worked alongside Sly's father and the walrus McSweeney in the previous Cooper Gang. Dr. M in particular was in the role later taken up by Bentley. At some point, their partnership soured with Dr. M believing his potential was both being wasted and not being recognized in the Cooper Gang, when he saw himself as the superior one.
It is commonly theorized that Dr. M may have been the one that alerted Clockwerk and the Fiendish Five to Sly's father's whereabouts, causing the events of the first game. Considering Dr. M's loathing of the older raccoon, it remains a possibility.
Sly 3: Honor Among Thieves
In the action prologue, Sly organizes Bentley, Murray, and their new Cooper Gang members to launch a heist on Kaine Island. While sneaking about, Sly eavesdrops on Dr. M and one of his chimerical goons discussing the goon's mistake of imputing a cheap security code of 1234, prompting Dr. M to kill the goon via poisoning. Sly almost makes it to the Vault's opening when Dr. M intervenes, connected to a giant chimera that tries to crush Sly in its claws. Sly loses his cane in the process.
After flashing back to show the organization of the new Cooper Gang, the narrative returns to find Carmelita Montoya Fox and her gorilla mercenaries launching an attack on Dr. M's monstrous chimera to save Sly. Dr. M pleads his case (as he was "just trying to defend what's his") and promptly has the creature toss her away when she tries to arrest him for his attempt on Sly's life. Nevertheless, she defeats the giant monster in the ensuing battle.
Dr. M reveals other chimerical beasts at his disposal, such as when he attacks Dimitri with an angler fish-like beast when the marine iguana tries to retrieve Sly's cane and where Sly does aerial battle with Dr. M's whale with dragonfly wings. Eventually, the cane is recollected and Sly makes his way to the vault with Bentley and Murray watching over the Vault's entrance. Here, Dr. M appears and confronts the two, crudely dismissing Murray as a "caveman" and trying to convince Bentley to join him and forgo Sly. The turtle refuses to betray his friend, prompting Dr. M to attack-though he is held off by Murray and defeated by Bentley activating the Vault's security system. Nevertheless, Dr. M escapes further into the Vault and tracks Sly by means of a tracking device implanted on Sly's cane.
In the Vault's innermost sanctum, Dr. M tries to kill Sly while speaking of how callous his father was. Sly argues otherwise, stating that his relationship with Bentley is nothing like that, but Dr. M dismisses it and attacks. Following their battle, Carmelita breaks into the Vault, prompting Dr. M to attempt hurting Sly by killing her. The raccoon takes the shot intended for her and Carmelita finishes the fight with shock pistol blasts. Carmelita escapes with an amnesiac Sly (in reality, he fakes it so as to be with her) while Dr. M remains behind, perishing as the Cooper Vault's rock walls collapse around him.
One noticeable quality of Dr. M is his intellect which rivals Bentley in terms of gadgetry and mechanical know-how. He also demonstrates a knowledge of creature splicing, as evident by his chimeras serving as his guards, goons, and monsters. But of course, this also entails a level of arrogance as Dr. M believes himself to be superior to the "lesser minds" like Sly.
It's also implied that he genetically modified his own body, since he was strong enough to wrestle with Murray, the powerhouse of the Cooper-gang. Not to mention that he seemed almost unkillable, as he survived getting shot, electrocuted and knocked of a blimp. In the end, he didn't die until an entire mountain collapsed down upon him.