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alternatehistory.com
This alternate timeline requires quite a bit of changes, so here we go:
The Army of the Orient comes prepared for their marches through the Egyptian deserts (i.e. lighter clothing, more water).
The Order of St. John (of Malta) accepts the French fleet, so that Russia doesn't become angry at France for invading the island.
The amphibious landing in Egypt isn't completely screwed up.
Horatio Nelson doesn't pull off his miraculous victory at the Battle of the Nile.
Napoleon is victorious at the Siege of Acre.
Murad Bey doesn't die just as he was about to join the French side.
Kléber is never assassinated.
With all those factors combined, I think Napoleon might be able to establish a permanent French base of influence in Egypt. Being that Murad Bey (partially) ruled Egypt, he might be able to quell Egyptian anger at the French occupation. Without the defeat at the Battle of the Nile, Napoleon's army wouldn't be marooned in Egypt with no reinforcements or supply chain.