Malice has to save her friends from the fairy tale parasites infesting their souls.
They have each been combined with the fairy tale that bit them. This has caused them to become hybrids—the Mad Hatter, for instance, is now half Cinderella.
To drive the fairy tale portion out, Malice has to drive a stake through their hearts. So, ironically, to save them, Malice essentially has to fight and kill her friends—the Mad Hatter, Tweedle twins, Humpty and the Knight. Hopefully, afterwards, Wonderland will finally get back to how it was before the twisted fairy tales came around.