You can enter the violet flowers to heal while shrunk. When Alice approaches them, their uncannily hand-like stamens start make grasping moves. Upon entering the flower, the petals close around her and health steadily recovers. Case in point, what the hell can a flower's stamens do to a teenage girl to restore her mental health???
Actually, there is more to that. The less health Alice has, the closer she is to Hysteria. Now, up to XIX century there was a trusted and tested method to cure female hysteria - 'pelvic massage' until 'hysterical paroxism'. Ahem.
So, the violets represent Alice's sexual frustration?
Most unlikely because side conversations in the London parts about Alice include how she doesn't like being touched.
By that point, Alice is about eleven different types of crazy. Not so unreasonable to assume that she could be both sexually frustrated and not like being touched. Also, A Date with Rosie Palms...
Okay gross, true but gross.
It could be that the closing of the bud, not involving the stamen, gives Alice a meditation sphere. Something like a Cooldown Hug. Also the flower's color might produce blue lighting which has proven calming effects. There is also the fact that the flower is of tropic origins: elongated stamen is common in wetter regions.
Maybe there's a chemical explanation, and the movements are merely symbolical (like how Alice obviously doesn't pick up teeth just by standing near them, even though that's how the game mechanics work). We never see how she interacts with the plants once she's inside them, and they do disappear when she's done using them.
Had anyone noticed the dark ring around the screen when London Alice obviously hallucinates? They might prove helpful of separating real and imaginary.
Just how does Alice wind up in the River Thames after her first hallucination with Nurse Witless? She hallucinates that the nurse is the Jabberwocky, enters Wonderland for the first time, and when she reenters the real world she is somehow in the river. The only thing I can figure is that she fainted, and for some reason Nurse Witless dumped her body in the river.
When she's released from the cell, the guard mentions having found her wandering and muttering to herself in an alley during her last episode. She's likely wandering about and interacting with the real world during her episodes.
Ok, can we please discuss what the hell was up with the scene with Radcliffe? After his one cutscene we don't see him again for the rest of the game and there's no further mention of him. Alice just wakes up in a ruined, abandoned version of his house. He mentions in his cutscene that he once told Alice he suspected she may have had a larger role in the fire than she thought, and says that she then suffered a psychotic episode. Upon returning to Alice's POV, she says she wanted to rip his head off, as if the conversation in question just happened. Even if it did, why would Alice wake up in what appears to be a house that no one has lived in for years? She couldn't have been hallucinating Radcliffe because Nan Sharpe specifically says she'll take Alice to see him, so he must still be living there.
Because Alice is, to quote the police officer near the very beginning, "off [her] nut." Who knows what she actually did from that point on. We see her wake up in the abandoned house, and she leaves out the back way, and... statue of the Mock Turtle? Large mushrooms growing in toxic-looking pools in the corners of the streets?! A MASSIVE VORTEX OF TUMBLING ROCKS?!? The next time we see reality, we see her in gaol, as mentioned above, having rambled about a murder on Threadneedle Street (where she was, as that's where Radcliffe's home is) and cursing insects (possibly the Caterpillar, maybe the paper ants, almost certainly the wasps) and "the National Railway" (the Infernal Train in her mind, more likely). It's possible Radcliffe, seeing she was having one of her episodes, turned her over to police custody to limit the damage she could do to herself and others. Even if the other officer didn't think she was dangerous.
Were the Dormouse and the March Hare originally supposed to be in charge of each other's levels? Or maybe have part of each other's lines? When they threaten Alice, each has one line that would be more appropriate for the other. The Dormouse says he's going to crush you in a part of the factory characterized by vast vats of superheated metal, while the March Hare says "you're about to feel like a lobster that's been tossed into the boiling pot" in a level characterized by giant metal hands and feet slamming against walls, floors, and each other repeatedly.
So who exactly is the Queen of Hearts supposed to represent?
There's evidence that backs up the theories that she either represents Lizzie or Alice's younger self, and either character would make sense symbolically for different reasons. The caterpillar mentions that she now resembles someone whom Alice 'knew and loved', which technically could mean Alice's former self, but it seems more likely to refer to another person, such as a family member. Furthermore Alice addresses the Queen as 'my Lizzie' on the Infernal Train, and the Queen is the character to fill in the truth about Lizzie's fate. It's also been pointed out that Alice's memories associated with Lizzie in Queensland begin to draw increasing attention to a creepy suitor, suggesting that the Queen - Lizzie's Wonderland incarnation - was urging Alice to put the pieces together with regard to what happened to Lizzie.
On the other hand, the Queen's appearance is too childlike to resemble Lizzie, who would have been in her late teens when she died and whose face in the family photographs is portrayed as more oval and adult-like than the very young face of the Queen. This would back up the theory that the Queen actually resembles Alice's younger self, which would make sense as a manifestation of Alice's subconscious and repressed memories. But then, why have Alice address her as Lizzie? Or was it supposed to be deliberately ambiguous?