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George Merkert was the Assistant Special Agent in Charge (ASAC) of the Albuquerque DEA Unit, serving as the boss for Agents Hank Schrader and Steven Gomez. He is impressed with Hank's work hunting down Tuco Salamanca and recommends him for a transfer to Tri-State Border Interdiction Task Force.
Because of his close personal friendship with Gustavo Fring and Fring's history as a generous philanthropist and public booster for the DEA, he was skeptical of Hank's notion that Fring might be involved with the criminal drug trade. After Hank's theories were revealed to be true by the discovery of Gus' Drug Empire and Gus' kingpin status, George Merkert lost his job.
When Hank returns, Merkert is frustrated by Hank's stalling on a second transfer to El Paso, unaware that Hank is suffering from panic attacks and is scared to go back. After Hank attacks Jesse Pinkman, Merkert is forced to suspend Hank without pay, but tells him off the record that Jesse won't press charges and that Hank must have a "guardian angel". ("One Minute") Notably, this leaves Hank without his gun.
Merkert listens to Hank's suspicions that Gustavo Fring might be the meth kingpin they've been looking for all along. Merkert, Gomez, Hank, and Tim Roberts interview Gus in relation to the death of Gale Boetticher; however, all but Hank fall in with Merkert and believe that Gus is telling the truth. Merkert in particular is insistent that Gus is an honest man and a long-time friend of the DEA.
In the last episode of Season 4, he also appears at the meeting between Hank and Hector "Tio" Salamanca.
Early in the fifth season, it is revealed that Merkert has been forced out as head of the DEA because of his personal friendship with Gus and his failure to identify him as a drug lord. ("Madrigal")