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When he was liberated and became a Resistance member, he became the captain of Pequod. He had an idea to visit the surface and collect artifacts of human history before the Machine War in order to reconstruct their past. He thus became the first Collector and a legend among the kids of Zion, as battling sentinels and surviving for weeks in the inhospitable deserted cities. But then he lost the ship and his crewmen to a Sentinel and drove him mad.
By the next year he joined the crew of the Polaris although he now was reluctant, knowing that the past civilization would mean nothing to a Zionite. Nova of the Polaris admired him and followed him in his last expedition where he was ready to die battling a sentinel with a spear, surgically hitting and cutting its tentacles, however he was torn by it.
After his death, Nova was left alone but managed to best the sentinel and buried Flint along with the other crewmembers of the Pequod but decided to not mention his death to Zion and let his legend go on.