Hunter was a clone commando sergeant of the Grand Army of the Republic and the commanding officer of Clone Force 99, the experimental squad of genetically enhanced clones nicknamed "the Bad Batch." Grown on Kamino from the genetic template of Jango Fett, he carried a mutation that gave him extraordinarily heightened senses — able to track targets by scent, sound and electromagnetic fields — which made him the squad's scout and de facto leader alongside the super-strong Wrecker, the analytical Tech and the sharpshooter Crosshair. During the Clone Wars he led the Batch on high-risk operations, most notably the campaign on Anaxes where they recovered the long-missing ARC trooper Echo from Skako Minor and folded him into the squad. Because their aberrant genetics left them largely immune to the inhibitor chips, Hunter and most of his men did not carry out Order 66, and their refusal to fire on civilians turned them into fugitives from the new Galactic Empire. On Kamino he took responsibility for Omega, an unaltered female clone, and the pair became the emotional center of the squad as they scraped out a mercenary living, lost Crosshair to Imperial conditioning and later lost Tech entirely on Eriadu. Hunter's driving goal became finding Omega a safe home, which he found on the island world of Pabu, and after storming the Empire's cloning facility at Mount Tantiss to rescue her and the other captive clones, he settled there. Years later he let Omega go to join the Rebel Alliance, remaining on Pabu with Wrecker and a reconciled Crosshair.
Hunter is created on Kamino as part of the first generation of Jango Fett clones, one of a handful of "defective" units whose mutations were deemed advantageous. His alteration grants him superhumanly acute senses. Like all clones he is engineered to age at twice the normal rate.
With the war between the Republic and the Confederacy underway, Hunter and his squadmates Wrecker, Tech and Crosshair are formed into Clone Force 99, named in honor of the malformed Kaminoan maintenance clone 99. Their unorthodox methods earn them a reputation for taking missions regular clones cannot.
Assigned to assist Captain Rex, Anakin Skywalker and Ahsoka Tano on Anaxes, Hunter leads the Batch on a raid of a Separatist cyber center. He then agrees to Rex's mission to Skako Minor, where the squad rescues the presumed-dead ARC trooper Echo from Wat Tambor's captivity.
On Kaller, Hunter's squad witnesses clone troopers turn on Jedi General Depa Billaba. Their mutations leave them largely unaffected by the inhibitor chips, and Hunter shields the Padawan Caleb Dume rather than hunting him. Only Crosshair complies with the order.
Returning to Kamino under the new Empire, the Batch refuse to fire on civilians on Onderon and are imprisoned. Hunter takes in Omega, an unaltered clone girl, and leads the squad's escape — leaving behind Crosshair, whose chip is intensified by Imperial doctors. They begin a fugitive life running jobs for Cid on Ord Mantell.
Lured back to Tipoca City by Crosshair, Hunter and the squad narrowly survive the Empire's orbital bombardment of the Kaminoan cloning facilities. Crosshair saves them but refuses to leave with them, and the clones' birthworld is destroyed.
After breaking with Cid, the squad discovers the island world of Pabu. Hunter, increasingly focused on giving Omega a childhood rather than a war, decides it should become their home.
During a mission on Eriadu to help Clone Captain Howzer, Tech sacrifices himself so the others can escape, falling from a collapsing rail line. Shortly afterward Omega is captured by Imperial forces and taken to Mount Tantiss.
Hunter and Wrecker search relentlessly for the hidden Imperial facility, eventually joining forces with a defecting Crosshair after Omega helps him escape. Hunter is briefly captured himself before being rescued by Omega, Crosshair and Wrecker.
The Batch infiltrate Dr. Royce Hemlock's cloning complex on Weyland, free the captive clone children and Omega, and destroy the facility, ending the Empire's Necromancer cloning program. Hunter, Wrecker, Crosshair, Omega and Echo survive.
Hunter settles on Pabu with Wrecker, Crosshair and Omega, laying down his armor and living the peaceful life he had fought to secure for her.
Years later, a grown Omega tells Hunter that the coming fight against the Empire is hers, not his, and departs Pabu as a Rebel pilot. Hunter watches her go and remains on Pabu with his brothers; canon records nothing of his fate afterward.