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In 1589, the Ottomans attacked Mombasa. The Ottomans were actually at a fairly advantageous position initially, but this was ruined by a wild card arrival of supposedly 20,000 warriors from inland Africa. The battle ended in a total defeat for the Turks, with their admiral, Mir Ali, apparently still in a Portuguese dungeon by 1608. Muslims would not regain Mombasa until in 1698.

What if the Ottomans won at Mombasa? I'll just quote The Ottoman Age of Exploration, which does a better job of summing up the circumstances:
With all of these advantages in his favor, what might have happened had Mir Ali and his allies managed to prevail at Mombasa in 1589? Supposing the Ottoman plan had worked, and Tomé de Sousa Coutinho and the Portuguese fleet had actually been defeated, it seems at least conceivable that Mir Ali would have eventually forced the capitulation of Malindi, Portugal’s last local ally, and from there taken possession of the entire Swahili Coast. Th is, in turn, could have allowed Hasan Pasha to present Sultan Murad III with irrefutable evidence of the merits of continued expansion in the Indian Ocean, silencing naysayers and finally ensuring a steady stream of material support for continued campaigning in the south. In time, the Ottomans might very well have extended their rule as far as the Zambezi River (or “the mines of Cuamá” in the language of the Portuguese sources), seizing control of the lucrative trade in gold, ivory, and slaves from the African interior and depriving the Portuguese of this crucial source of revenue. Thus weakened, it is an open question whether the Portuguese could have maintained control of Mozambique, and it is even more uncertain how they could have faced the coming challenge from the Dutch in the following century. In short, under only slightly different circumstances, Mir Ali’s expedition to the Swahili Coast could quite possibly have spelled the premature demise of Portuguese Asia and ushered in an entirely new era of Ottoman dominion in East Africa.

Of course, the Ottomans still faced major structural issues by this point, not only with their maritime presence in the Indian Ocean but with the empire in general. But with all this in mind, what would have happened had Mir Ali routed the Portuguese fleet in Mombasa?
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