Napoleon abandoned them. The army was defeated by a coalition of British and local troops. They surrendered to the British who took the officers as prisoners and repatriated the soldiers to France.

Well Berthier, Murat, Lannes, and Marmont all went with Napoleon when he fled Egypt (and Dumas had left previously), so the only officer of note who remained was Kleber, and he obviously wasn't happy about it. The troops were very angry as well, to the point of revolt, but Kleber soothed them by claiming that Napoleon's absence was only temporary and that he would return after settling matters in France, which obviously never happened. Kleber won a few victories against the Mamluks after Napoleon left, and after his assassination in 1800 command passed to Menou, veteran of the Vendee, who surrendered to the British in Alexandria in 1801, which is how the Rosetta Stone ended up in the British Museum instead of the Louvre.