Protecting the human settlers of Pandora necessitated keeping the local indigenous population of Na'vi in check. To this end, Quaritch enlisted a young Marine, Jake Sully, for a covert operation -- infiltrating the highest ranks of the Na'vi in order to provide actionable intelligence towards their pacification.
As time passed, Quaritch grew suspicious of Jake's increasing affection for the Na'vi, particularly Neytiri, daughter of Eytukan, grand patriarch of the Omaticaya Clan.
Jake's allegiance, not to mention his sanity, was called into question after one notable incident in which -- in a fit of rage (and, it is suspected, under the influence of Pandoran psychotropics) -- he proceeded to attack a bulldozer.
Disappointed with the Na'vi's resistance to diplomacy and abject refusal to relocate from their Hometree (a geographical locus of the insurgency), Quaritch embarked on a campaign of "relatively humane" measures to evict its occupants.
The security operation involved the initial firing of gas and incendiary rounds to flush the Na'vi from their command post, followed by a hail of rockets culminating in the Hometree's structural destabilization. Unfortunately, the action resulted in several incidents of collateral damage -- including the death of Eytukan.
The collapse of the Hometree and the unfortunate demise of the Omaticaya Clan's leader led to mass rebellion amongst the Na'vi, the mutiny extending beyond the Na'vi proper to the wildlife of Pandora itself.
A subsequent exploratory convoy, again led by Quaritch, met with an ambush. Heavy casualties were inflicted on his forces by Jake (now wholly aligned in mind and spirit with the Na'vi insurgency).
Aircraft downed, separated from his men and engaged in fierce hand-to-hand combat against insurmountable forces, Colonel Miles Quaritch ultimately fell to the arrows of the Na'vi.