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The Heretic Unggoy followed their Sangheili organizers in a rebellion against the Covenant's Prophets. They started as members of an artifact retrieval group led by the Sangheili Sesa 'Refumee. When he and his Sangheili chose to rebel against the High Council after being informed of Halo's true purpose by 343 Guilty Spark, the Unggoy in his command followed them. They do what they can to stand out from the Covenant, especially other Unggoy.
These Unggoy have different methane tubes than their non-Heretic counterparts. They have just two blue-white glowing round tubes, instead of the pointed-pyramid shape. Another feature of the Heretic Unggoy armor is a small mouth-breather that exposes an Unggoy's teeth.
Unlike the armor of the Heretic Sangheili, there is only one uniform color for the Unggoy's armor, which is a shining, golden-brown. Because of this, there is no hierarchy or ranking system, and Heretic Unggoy are inferior only to Heretic Sangheili.
Heretic Unggoy fight differently than the Covenant-loyal Unggoy normally encountered by one fact: They never try to escape, even during Easy difficulty. The only exception to this rule is when a Heretic Unggoy is stuck with a plasma grenade, needles, or otherwise knows it will soon die; even then, they will run towards you, setting the precedent for Kamikazes in Halo 3.
They are also superior to their average Covenant counterparts (Minor and Major Unggoy) by their equipment and usage thereof (though Special Operations Unggoy and Unggoy Ultras are equally skilled if not more). They almost always use Needlers, or occasionally fuel rod guns, but never the weak, inaccurate plasma pistol that is so often overused by their counterparts. They also try to set up turrets sometimes like Special Operations (or "Heavy") Unggoy. Beware, their skill with the Needler is unchallenged; they fire incredibly quickly, accurately, and reload when taking cover. They are also very good with their plasma grenades, capable of sticking unsuspecting Special Operations Sangheili frequently.
They are also far harder to kill than the average Unggoy. Any Heretic Unggoy can take as much damage as an Unggoy Major. They do not come in ranks, and all have the same amount of health and intelligence as each other. The only difference in difficulty facing them is the weapons they carry. Depending on what weapon you are better against will usually depend on how hard it is to beat the Unggoy. In combat, Covenant Unggoy will usually be encountered in groups of four or more, whereas the Heretic Unggoy are normally in smaller groups, of about four or less. Heretic Unggoy are also harder to melee because of the reduced size of their methane tanks. In fact, in Legendary, they can take as many body shots as you can. They are still vulnerable to high-power weapons like the energy sword, and rapid-fire weapons like the Needler or Sentinel Beam.
Their intelligence also shows that they are well trained and well educated by their Heretic leaders.
Concept art for Heretic Unggoy for Halo 2: Anniversary.