This discussion may contain spoilers!
So working with the help of Kroms's bullet points, I have worked out what I think to be the Grand Backstory behind TMI. Master Plans and all are revealed here! SPOILERS AHEAD!
PLEASE NOTE: This is a REVISED version of the original post, in which I have modified my theories to incorporate things pointed out by fellow forum members.
So some time before Narwhal, Guybrush gets the Cursed Cutlass of Kaflu recipe from the Voodoo Lady. (One of the dialogue options on first meeting her in Narwhal is "That cutlass recipe you gave me was a dud!" though Guybrush never says it out loud.)
However, this Cursed Cutlass would inevitably, when used, fail to kill LeChuck. Even if Guybrush hadn't tampered with the recipe, it would still fail because he isn't attacking LeChuck while he's crossing between worlds. This is intentional on the Voodoo Lady's part.
The Voodoo Lady desires to keep Guybrush and LeChuck eternally at each other's throats. By the end of Rise, she possesses Guybrush's poxed hand and an essence of LeChuck, which combined are enough to resurrect BOTH of them, if either should die, thus continuing the cycle infinitely. (Remi Olsen has pointed out that she was already seen shipping voodoo supplies to LeChuck in MI2!)
Elaine does NOT know at first that the Cutlass of Kaflu is destined to fail, since she tries to use it herself on LeChuck at the finale of Rise. Nor does she know yet that, to kill LeChuck, you need the help of someone standing on the other side of the Crossroads. (Guybrush has to tell her this in Rise.)
However, by the end of Rise she clearly believes that the Voodoo Lady is up to no good. The feeling is mutual. In the seagull scene in Rise, the Voodoo Lady calls Elaine a "loose cannon" who "does not trust in Voodoo." She's telling a half-truth in this last statement: Elaine does in fact trust Voodoo, just not the Voodoo Lady's voodoo.
Elaine has probably suspected the Voodoo Lady of nefarious deeds for a while now, since in Rise she says that she first let LeChuck capture her in order to demonstrate this to Guybrush. Most likely, though, she fully grasps how bad the Voodoo Lady is after LeChuck is humanized and the Pox is released.
Once she has been captured, Elaine watches Guybrush use the cutlass on LeChuck, not knowing for certain but half-suspecting it won't work at all, and hoping that Guybrush now realizes that the Voodoo Lady has been lying to him all along. He doesn't, of course.
LeChuck is turned human, and although Elaine knows he is still nasty and evil, she hopes to use him to get at the Voodoo Lady (by, for example, obtaining her diary). She doesn't tell Guybrush, of course. But she is thrown off her guard, and lulled into security, by the evil Voodoo of his belt buckle, and fails to adequately make plans for his eventual betrayal of them in Trial.
Elaine doesn't know yet that LeChuck can only be killed once he is crossing between worlds. But she goes along with LeChuck's plan to "give the monkeys new homes," even though she suspects it's all a lie, at least in order to convince him his disguise is working (as noted, the belt buckle clouds her judgment).
The Pox is released, and then Guybrush turns up with a quest from the Voodoo Lady to go after "La Esponja Grande." This is probably where the pieces all click together for Elaine. Since she knows Human LeChuck is still evil, she is certain that, once La Esponja absorbs all the voodoo energy of the Pox, LeChuck will simply take the sponge and reabsorb the voodoo into himself. She also knows that the Voodoo Lady PLANNED this to happen.
When Guybrush loses his hand to Morgan (and his wedding ring with it), Elaine supplies him with her ring instantly. She doesn't know EXACTLY what he'll need it for, but she DOES know that wedding rings are powerful items in voodoo spells, because of the pure love they represent. She wants Guybrush to be magically protected in case the worst should happen.
Elaine is blindsided by LeChuck killing Guybrush (which she WOULD have foreseen were it not for the demonic belt buckle). She didn't want Guybrush to enter the Crossroads by actually DYING.
Then once Guybrush returns as a ghost, LeChuck announces that the Cutlass of Kaflu is the only weapon that can kill him in the mortal world, and that he has enchanted it so that no mortal can touch it. Elaine is immediately seen going "Hmm!" Her next line after that is to LeChuck: "Make me your demon bride!" or some such.
Elaine obviously decides on the spot to become a demon, so as to get her hands on the Cutlass, and is counting on Guybrush (as she says in the very end of Rise) to restore her afterward, so she can kill LeChuck with the blade. (I guess she expects to keep holding onto it as a demon until she's exorcised!)
In other words, Elaine's master plan was never set in stone, but has had to change in numerous ways, due to unforeseen events. Such events included the Pox being released, or LeChuck surviving as a human, or Guybrush losing his hand, or LeChuck killing Guybrush (a major unforeseen event!), or LeChuck cursing the Cutlass to make it unusable by mortals.
When Guybrush is punted back into the Crossroads by LeChuck, Morgan shows up after an extended absence and stabs him with a new sword. Guybrush asks where she got it but she doesn't answer.
Answer: The Voodoo Lady gave Morgan the sword, in exchange for her retrieving LeChuck's essence after dispatching him. The Voodoo Lady wants to kill LeChuck for the moment, so that Guybrush will be lulled into a false sense of security and think LeChuck is finally truly dead. She knows, however, that if Morgan does her job right, she will soon have the Essence of LeChuck with which to revive the demon pirate at a later date.
LeChuck's plan, of course, is much simpler: Hypnotize the 13 Monkeys of Montevideo and place them at specified locations in the Caribbean, so as to reveal the physical location of the Crossroads in the mortal world, allowing him to crack it open, suck out its energy, and become the Demon Pirate God. Needless to say, his scheme fails until Guybrush unwittingly helps him out.
NEW EDIT: After input from commenters, I've rewritten this so it's somewhat more plausible. People have pointed out that I thought Elaine knew far too much, and I think they're right!