Complex sentence: Marakkar, who had been given the powers and privileges of any Nair noble in the Samoothiri's service, strengthens the fortress at Kottakal and openly challenges his master by styling himself as the "Lord of the Indian seas" and "King of the Mappilas".
Split into simpler sentences: Marakkar, who had been given the powers and privileges of any Nair noble in the Samoothiri's service, strengthened the fortress at Kottakal. He then openly challenged his feudal overlord, the Samoothiri, by styling himself as the "Lord of the Indian seas" and "King of the Mappilas".