Miller and some of the other survivors of MSF eventually reformed as the Diamond Dogs. During the nine years Big Boss was in a coma, Miller spent his time training various dissident soldiers.[66] During this time, he was referred to by the Diamond Dogs soldiers as Commander Miller. In 1984, Miller was training some Mujahideen soldiers in Afghanistan during the Soviet invasion, with his also having the personal motive of hunting down Huey, as he had heard that Huey was at the Afghanistan Central Base Camp. However, he and his unit were ambushed by the Parasite Unit, which eventually resulted in his unit being killed, him losing his right arm and left leg, and him being captured and tortured by the Soviets. Before his capture though, he told Ocelot to seek out "Big Boss" at the hospital, both to rescue him from a similar attack, but also so he could save him. Miller was later found chained up in a house by Venom Snake, who helped him to escape the country on March 21st, 1984.
Venom Snake helps Miller to walk, after saving him in Afghanistan.
Miller shortly recovered and was given a prosthetic leg and a cane to help him walk. Although Ocelot suggested that he get some Soviet-made prosthetics to replace his lost limbs, Miller declined, stating that he didn't care for his limbs anyhow and that he wanted to at least live with his phantom pain until his comrades were properly avenged. The attempts to destroy MSF, combined with the suffering endured during captivity, made Miller extremely vengeful towards Cipher, more specifically XOF and its leader Skull Face, and obsessed with its destruction. Although he wanted Diamond Dogs to be based in Latin America over Seychelles, he ultimately accepted the latter, as Latin America was doing fine under Amanda.
Miller then began to undertake his duties as Mother Base's XO, being in charge of all of Mother Base while Venom Snake went out on missions. Among his first duties was providing a list for Snake via the iDroid regarding which missions they have accepted they should do first, citing that they'll have to get their hands dirty if Diamond Dogs is to complete their objectives.[67] Miller, along with Ocelot, provided tactical support for Venom Snake whenever the latter was out in the field, giving him advice on how to achieve his objectives and advising him on the multiple courses of action Venom Snake could take. At some point after their new Mother Base received extensive expansions, one of their forward operating bases ended up invaded by a competitor. He later notified Venom Snake of this as soon as he returned upon receiving the news, and requested orders from him in a way that made clear he was very eager to find the intruder and teach them and whoever they worked for a lesson. After several successful missions in Afghanistan, Miller received a coded transmission from a man he had been hunting for years, Huey Emmerich, who wanted to defect from mysterious military group XOF over to Diamond Dogs.
Believing that Huey was somehow involved in the attack nine years earlier that destroyed MSF, Miller insisted that they agree to Huey's request so that they could interrogate him about his whereabouts during the MSF attack. Venom Snake then headed to the Soviet occupied Serak Power Plant where the transmission was sent from, but was sidetracked by the sniper Quiet who began shooting at him. Miller, not wanting Huey to disappear, advised Venom Snake to sneak past Quiet and return later. Upon arriving at the facility, Venom Snake snuck his way past the Soviet troops stationed at the plant and discovered a hidden XOF facility housing a Metal Gear, although Miller reminded him that the priority was Huey. Venom Snake then caught Huey discussing the Metal Gear with the XOF commander, Skull Face, on the facility's checkpoint tower. Overhearing their dispute after Skull Face learned of Huey's betrayal, Miller advised Venom Snake to go after Huey before he was executed.

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RandomMy pupil Snake has one so why not? get with the times I suppose