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Following the Battle of the Nile (Aboukir Bay), the bulk of the British fleet, including Nelson's flagship Vanguard, returned to the western Mediterranean (either to Gibraltar or to Naples) in order to repair and refit. Only a small covering naval force under Sir Thomas Troubridge was left to blockade the French transports in Alexandria. This small flotilla was supplied from friendly Ottoman bases in Cyprus and Rhodes.
Troubridge was replaced by Sir Sidney Smith as, effectively, the naval commander in the region. It was under Smith that the British forces assisted at the Siege of Acre. The bulk of this assistance was in the form of gunfire support from HMS Tigre, HMS Theseus and some smaller gunboats. However, some marines and gunners from the two ships of the line were landed to fight from the city walls, with the Ottoman defenders. So there were no "land troops" as such, simply naval personel operating on land.
Additional info can be found in the answers to How did Napoleon evade the British fleet and return to France?
Wtih regard to the later campaign in Egypt, I think it's probably inaccurate to describe the British forces as occupying those cities. Since that implies that they had political control. They were allowed, by their Ottoman allies, to garrison forces there but they were not considered to be British territory.
Finally, Cyprus was under Ottoman control at the time. It only came under British control in 1878.
(And SEGA were the publishers of the game, it was invented by the Creative Assembly, a British software house)
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It is important that even though Napoleon was beginning to have land superiority in Europe after the Revolutionary wars, the extent of Royal Navy's reach was far superior than that of French Navy. Specifically, Royal Navy had a Mediterranean Fleet, with a base in Gibraltar. That should more or less answer the first question.
As for the second question, it seems like (see this) the role of British forces in the Siege of Acre was providing cannon firepower from the Royal Navy ships HMS Tigre and Theseus, whereas the land army was Ottoman. British also trained some Turkish forces, but the infantry was mainly Turkish, and not British.
For the last question about British possession of Cyprus, it is not true. British took control of Cyrpus after Russo-Turkish War of 1877-78. It was under Ottoman control before.
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The French campaign in Egypt and Syria had ended by August of 1801, with their defeat and surrender at Alexandria. Napoleon had abandoned them two years previous, when he returned to France, and reorganized the government in a coup against the Directorate.
Where did the British troops used against the French in Egypt and Syria come from? In the earlier events they were marines and crew of the British fleet, which had total control of the Mediterranean following their destruction of Napoleon's fleet at Aboukir bay, the Battle of the Nile. Battle of the Nile, Thomas Luny
Note that the Ottoman Empire was also at war with France, and there were many forces at work here. The use of the British sailors and marines, landed from the fleet, was very common when the British fleet had local control of the seaways.
By 1801, the British fleet had transported an expeditionary force to Egypt, beginning the the Battle of Abukir (March 1801), the defeat of the French forces at the Battle of Alexandria, and finally the Siege of Alexandria, which ended with the surrender of the French forces.