On the third day he decided something must be done about the hierarchy aboard the Endeavour:

Lord Beckett had no business commanding a flagship, Groves chaffed at being 1st Lt. and rubbed everyone the wrong way, and 2nd Lt. Greitzer was far more suited to captaincy. Norrington would usurp the staterooms, appoint Groves Master and Commander of a reconnaissance sloop, and elevate Greitzer to flag captain; it would not be the last time James was grateful for the power of his new rank.

Furthermore, he needed loyal men aboard his flag ship. Two marines came to mind, Murtogg and Mullroy.