Like most of the Wonderland creatures, the Mad Hatter's physical appearance has drastically changed. He is now green-skinned and wears what looks like a loosened strait jacket that has a large gear protruding out of his back. He wields a cane and his hat has changed, being taller and covered in astrological symbols. The Hatter resides in a giant glass clock container, his laboratory and a warped version of Rutledge Asylum hidden underneath where the Tweedles, and the Hatter's victims, lurk.
American McGee's Alice
While Alice and the White Rabbit were seeking out the Caterpillar in Wonderland Woods, the Mad Hatter killed the Rabbit, crushing him flat beneath his foot, as Alice and he were a small size at the time. Alice, after killing the Red King, was then kidnapped by the Mad Hatter, who she confronted in his hideout and killed, his head exploding due to his mechanical body malfunctioning. Though not revealed in the game, the Deadtime Watch Alice discovers after killing the Mad Hatter is a recalibrated version of the White Rabbit's pocketwatch. The Mad Hatter is also presumably responsible for having repaired the Jabberwock by replacing body parts with metal and machinery, having been left drastically disfigured by the Vorpal Blade. The Hatter is referenced to in the casebook of Dr. Wilson, Alice's doctor. The asylum's superintendent is described with similar traits as the Hatter and his two nephews are orderlies who torment Alice- a reference to the Hatter's henchmen, the Tweedles. He is revived when Alice regains her sanity, apparently regaining his own as well or at least enough to return to his harmless former ways.
Alice: Madness ReturnsThe Mad Hatter returns in the sequel, his steampunk empire now ruled by the March Hare and Dormouse. Alice finds him in pieces, and collects his missing limbs in return for his aid in finding out what the March Hare and Dormouse are up to. The two discover the Infernal Train as it leaves the factory, the Mad Hatter angrily killing his old friends only to have a change of heart and attempts to revive them. He and his friends seemingly perish when the factory collapses around them. The Hatter reappears, however, near the ending of the game, aboard the Infernal Train, where he scolds Alice for the darkness and ruin she let onto Wonderland.