- For Voyager's Maquis first officer with a similar sounding name, please see Chakotay.
When a group of Bajoran extremists, the Alliance for Global Unity, attempted to seize control of Deep Space 9 in 2370, he ordered the station evacuated, citing the Prime Directive of non-interference. He gave this order even though there was evidence that this extremist faction was in fact backed by the Cardassians, telling Benjamin Sisko it was "a hell of a turn", with the possibility of losing Bajor and the Bajoran wormhole. (DS9: "The Circle")
Later that same year, he allowed Commander William T. Riker to delay a mission of the USS Enterprise-D in order to investigate the apparent death of Captain Jean-Luc Picard at the hands of a group of mercenaries while on an archaeological excursion to the planet Dessica II. (TNG: "Gambit, Part I")