The Emperors 'To Do' list.
Hmm. I originally meant to write something funny here, and just starting typing away like it was a logic problem. Sorry.
One thing that is missing here is that fact that way, way back in the fluff its stated that the Emperor is a giant leap forward in the evolutionary path of humanity. Now if we assume that such is the quality of his mind that he hasn't gone totally raving....
It seems to me that his goal has always been to protect humanity until the race accends to his own level and to sheppard them in that direction. The trap that Chaos holds for humanity is the stumbling block beyond which most are either caught in, or fear to rise higher due to the chance of being 'corrupted.' Therefore I feel that he would have bigger fish to fry in the long run than mere physical conquest. That was always an ends to a means.
1.Convince folks that he is indeed the emperor. This would indeed take quite some time due to the size of the galaxy and the aforementioned schisms arising.
2.Solidify his control of the Empire. A long and wideranging goal...Probably start with the Marines, as they still owe fealty directly to him. Good to have them on his side for all the work he has ahead. Keep the custodes around as well, as its always good to have bodyguards...
2a. Go to Mars, oust the Dragon, purge followers of the Dragon and kick people in the ass until they started scientific expirimentation again, rather than mere duplication and reverence for the past. Maybe relay some actual information of his own to help them along.
2b. Reform the Eccleisiarchy. I won't go into this, as I'm sure everyone has different ideas of exactly what this would mean. But I think we can all agree that he's see changes needing to be made. Mankind cannot ascend to the next level if it is stuck in reverence of things that are not actual gods.
2c. Get the Eccleisarchy forces firmly under his thumb, make examples of people who doubt him as being the Emperor. He'd probably have to play up the 'divine' emperor bit for quite a while here, even if he didn't like doing it.
2d. Purge/reform the Inquisition. HARD task, as some of the greatest threats to his rule would be in it. Need to keep it intact, however, as Chaos is still ever present.
2e. Get the High Lords of Terra firmly in hand, or better yet appoint new lords and send the ones in power to 'noble tasks' like attacking the Arch Arsonist of Charandon or whatever. He'd probably run into difficulties if he had them killed unless they directly opposed him.
2f.The Navigator families would be extra important now with the Astronomicon either gone or weakened due to his corporeal presence, so he'd need to make sure of their loyalty and get them breeeding...
2g Make a list of the threats to the Imperium and Mankind and go after them in order of either ease of elimination or of danger. Hard to say which is which here, but I think that the Emperor would find that the big three are Chaos, Necrons and Tyranids. And in that order I think he'd go after the Necron first, the Tyranids second and Chaos third.
Yes the Orks have more numbers, but they will always be around due to the ease of their breeding and you can generally count on them to fight each other. Dark Eldar/Eldar, not big in numbers, sometime allies. Now, there's not too many Necrons active now, but that will soon change, and for that reason their planets should be attacked now before they become fully active. Secondly, the technology to be gained in a full scale war with the Necrons would help with fighting both the Tyranids and (if the necron fluff is accurate) with weapons that would help combat warp intrusions into realspace. The Tyranids need to be attacked with overwhelming force as soon as possible, so that they do not build up a surplus of biomass, and to help convince the (various?) hiveminds that more effeicient pickings are to be had in other galaxies. Flesh that fights is after all, harder to digest that flesh that doesn't. After these threats are dealt with, and only then would the Emperor turn to the threat posed by Chaos. Not because it would be easiest to defeat, but rather the hardest, since it would breed fifth columns in his own forces and is bred into the very genes of humanity. Only with all external threats are defeated, and its own internal strcucture strengthened could Humanity deal with the threat that Chaos poses.
However. The method by which such a threat might be eliminated would not be by outright battle. Even if all the servants of the Chaos Gods were killed, the Gods themselves would be strengthened by the very deaths and passions that such a war would generate.
2h What is required is to raise all humanity to the level of the Emperor. Such a task would require both new technologies on the behalf on the behalf of the Technocrats(Any survivors would not be called Tech priests, such veneration of a machine 'god' degrades humanity), training and shooling of psykers directly by the Emperor ect.
The problem would remain though, that any humans so raised up above their fellows would begin to feel pride(like the primarchs) and might repeat the failures of the Horus Heresy. Other than attempting to raise the capabilities of all humans simultaneously, I don't see any way of achieving this.