Balak hates humans because they claimed territory and resources that he believes should have belonged to the batarians during the early stages of humanity's major expansion into the Skyllian Verge. He sees his actions as reprisal for the Skyllian Blitz on Elysium.
Balak rigged the fusion torches propelling the asteroid to execute burns that put it in a collision course with Terra Nova. After Shepard lands in the Mako and begins on shutting down the fusion torches, Balak sends his forces after the Commander. Balak then hunts for the hiding engineers in the main facility who were aiding Shepard. When he finds Kate Bowman, he demands to know who is attacking his people; when Kate refuses to answer, Balak kills her brother and sends Charn to find Shepard.
When the Commander launches an assault on the main facility, Shepard confronts Balak, who has planted a bomb in the offices where the hostages are being held. Balak talks angrily about the thwarted Skyllian Blitz (if Shepard is a War Hero, Balak holds Shepard personally responsible for the Blitz's failure) and about Torfan (if Shepard is Ruthless, Balak accuses Shepard of murdering batarians).
Shepard has a choice to make: either attack Balak to ensure his death, or release him in order to save the hostages, including Kate Bowman.
Balak detonates the bomb if Shepard chooses to attack him, killing the hostages, though he soon falls under the Commander's assault. Cornered, he taunts Shepard about the similarity of their actions, rhetorically asking the Commander "who's the real terrorist" now. Shepard can first fire a warning shot, graze him, then seriously wound him, or alternatively just verbally spar with him, but that doesn't stop Balak from spouting batarian jingoism, unless Shepard kills him outright.
Judging by Balak's reaction when Shepard asks him who is in charge of the batarians' terrorist actions, it is likely that Balak, as well as other batarian terrorist groups, answer to a higher authority. Balak's fate hinges on Shepard's decisions: he's executed after Shepard learns everything there is to learn from him, he's left to die there and then, or he's dropped off on Terra Nova to be handed over to the Alliance.