That was his goal as the leader of a French "empire", however butterflies will cause his goal to change. The most likely and logical choice would be to go up the Nile (away from British naval interference) and set up shop around Khartoum. Create a local empire. His military genius and superior weaponry will gain him quick victories, which will translate into having vassal states and the area has local iron that he can set up having some superior technology for steel than was local for Africa. He has some of the greatest scientific minds with him, they'll be loving being there, and will push him to get them to the mouth of the Nile, to explore Ethiopia/Aksum, and to look for these rumors regarding the "real" Ark of the Covenant being in a church in Ethiopia and there being remnants of the Lost Tribe of Israel there as well.
Napoleon showed himself to be very sensitive to local religions and he took pains to make the Muslims of Egypt believe he was one of them. He'd do the same in Nubia/Sudan. The British themselves could not hope in the early 1800s to have an expeditionary force large enough that far inland that could defeat Napoleon and his allies. If Mohammad Ali is not butterflied away (and he wouldn't be), then Mohammad Ali would be the one to take down Napoleon with British, Russian, and French help. If Napoleon is not able to reach some sort of recognition first in return to limiting his African Empire to only certain lands.