Headcanon for Alice’s Hattress dress:

The Mad Hatter attempts to open of of those gates in his domain to get to the giant mecha March Hare and Dormouse created.

A lot of enemies start to pop out so Alice has to defeat them while the Hatter tries to get the gate to open.

Alice defeats all but one enemy: a very sturdy Eye pot. The thing charges at Alice, bombards her with boiling tea and all the crap these mooks tend to do. Alice is pretty exhausted because she had to fight off a bunch enemies all at once, but she still manages to kill the remaining Eye pot.

…Or so she thought. Suddenly the Pot body slams Alice, sending her flying and causing her to hit her head really hard against the walls. This leaves her stunned for a few seconds, causing her mind to experience some very disturbing memories. In a fit of rage, she takes the Vorpal Blade and damage the Pot’s eye but to a terrible price. Just as Alice stabbed it, the Eye Pot used its metal legs to pierce Alice’s left shoulder. Alice is completely weakened all of the sudden that she has no energy left to go into Hysteria. There’s a lot of blood everywhere and she blacks out.

The last thing she remembers is the Hatter shouting “Hang in there, Alice! I’ll save you!”

Alice wakes up for a brief moment and, with blurry vision, sees the Hatter who tells her to stop being naughty and stay still. She faints again because she is completly weakened and drugged.

Alice finally wakes up and finds herself in the Hatter’s lab (where March Hare and Dormouse were held hostages in the first game). She asks the Hatter what happened. He’s tinkering with some of his former experiments and says that she was ridiculously defeated by a stubborn Eye Pot and that she hit her head really badly it shook Wonderland. He then shows her a pair of rusty scissors mentioning that her hair was getting in the way. Alice sits up and reaches her head. Her hair has been indeed cut very short (much shorter that her London hair).

She gets angry at the Hatter for chopping off her lovely locks she was very fond of (btw, the Mad Hatter mentions that Alice needs a hair cut in the first game; he finally got his wish). Just as Alice is about to call him more nasty names, The Hatter tells her that her new hairdo is the last thing she should be worried about. And then Alice looks over to her left shoulder.

And she turns pale.

The Hatter explains that the Eye Pot from before didn’t just stab her shoulder. It actually severed her arm. That’s why there was a lot of blood around and why she passed out so soon. The Hatter came to her rescue by smashing the Eye Pot with his teapot cane and dragged Alice to his lab. It didn’t occur to him to pick up the severed arm, so instead he built her a new one, made of used parts of his old robots and installed gears into Alice’s spine to allow movement of the new limb. He also fashioned her a new dress made out of a straight jacket to keep the arm in place. She was now an Automaton.

Alice was very shocked at first and about to have an emotional breakdown. Her severed limb was now rotting somewhere around the filthy domain, probably becoming the feast of the stray enemies that lived in the domain.
But then the Cheshire Cat told her to be thankful for losing her arm and not her head, so Alice decided to move on.

She told the Hatter to take her to the place March Hare and Dormouse were to deal with the Infernal Train.