Who was in charge in Egypt?

Muhammed Ali Pasha, an Albanian commander in service of the Ottoman Empire. He was ordered by the Ottoman Empire to re-occupy Egypt in 1801 after the withdrawal of Napoleon Bonaparte's forces.

It was a long clash between the Ottoman turks and the Mamluke Sultanate(the old Egyptian state from before the Ottoman Empire took over in 1517, still seeking to regain their rule and maintaining the power they still had.).

In 1805, a group of prominent Egyptians demanded that the current governor stepped down and that Muhammed Ali took his place. And later gave himself the title of Khedive(Viceroy) and declared independence from the Ottoman Empire as the Khedivate of Egypt (although not recognized). And in 1811 he murdered the remaining Mamluk beys to strengthen his control over Egypt.