How did England challenge Portugal in the Indian Ocean?

How could the Dutch and English challenge Portugal despite its Indian alliances and factories?

England largely cooperated with Portugal against the Dutch, and Portugal accepted English support because pressure at home made another war unaffordable.

English power did not initially enter the Indian Ocean only as an enemy of Portugal. England and Portugal could cooperate to push back Dutch competition. By the time England had sufficient regional strength to become a major threat, Portugal also needed English support against Spain and other pressures closer to home. Strategic dependence encouraged accommodation rather than a direct Anglo-Portuguese war for every factory and route.