While testing a new nuclear bomb defusing team at the Phoenix Foundation, a deadly explosion kills three men. Pete blames himself for not inspecting their equipment better and resigns from his job out of guilt. However, Pete is replaced by a not-so-trustworthy man—one who may have been connected to the explosion.

MacGyver returns to his home town of Mission City, Minnesota to meet up with two old friends, Chuck and Neil, so they can dig up a time capsule they buried twenty-five years before. However, MacGyver is hesitant to dig the capsule up because he is still haunted by the death of his old friend Jesse, who died when MacGyver was young. But now MacGyver has another problem to deal with. Chuck's and Neil's sons, Danny and Sean, have gotten wrapped up in a drug deal, and the dealer is after Danny. Danny takes off to hide, and now MacGyver must find him, before the drug dealer does.