Here is what we know so far:
Palpatine wakes up one day and decides to take over the galaxy. (pre-TPM)
Senator Palpatine enlists the Trade Federation to start a scuffle on Naboo. (TPM)
Palpatine wants Queen Amidala to sign a treaty with the Trade Federation. (TPM) Why does he need this treaty signed and what would the treaty actually do if it was signed? And how would a mystery treaty between Naboo and the Trade Federation aid Palpatine in taking over the galaxy?
The situation seems to work out in Palpatine's favor when Amidala escapes to appear before the Senate. Now he can influence her to be the motivating factor in removing Valorum from the Chancellor's seat, which happens. (TPM)
Now Palpatine is "in charge" of the Senate. (TPM)
Presumably, Palpatine enlists the help of Dooka and possibly Sifo Dyas to build a clone army. In political terms, what does this do for Palpatine's plan to take over? Why begin construction of the army before he knows for sure that he can "make it legal?" If his plans didn't work out (either through the bill to make it legal or by maneuvering his way into getting special executive powers) (b/n TPM and AOTC)
Nute Gunray, possibly with the urging of Palpatine, attempts to assasinate Amidala before she can stop the official go-ahead for a clone army (which is being constructed anyway). (AOTC)
With the assasination attempts thwarted, Palpatine gets Amidala to leave Coruscant believing that she will be absent during the critical vote and/or because he knows that simple minded Jar Jar can be influenced to hand over the special "executive powers" to Palpatine. (AOTC)
Palpatine specifically suggests that Amidala be protected by Obi Wan Kenobi. Why Kenobi specifically? Is he assuming that Anakin will be there too? Does Anakin's presence with Amidala have anything to do with his intricate plan? (AOTC) Has Palpatine already weaved Anakin into his plans at this point or by this point? What purpose would Anakin have for Palpatine in his "new order?"
Those are the main bullet points as far as I can tell. Jump right in to fill in the blanks if I missed any and fire away at those questions regarding the main highlights of his plan as we know it. Please don't just deal with only one of the points or questions as all of them relate to each other in chronological order. Please quote each bullet point and each question specifically and deal with them individually in order. Thanks!