In 2007, as the submarine was approaching parallel to the Island, one of Widmore's crewmen saw through the periscope eight people standing on the beach camp: Jack, Hurley, Sun, Frank, Miles, Ilana, Richard, and Ben. (6x07)
The submarine later docked at Hydra Island, where Widmore's team, led by Zoe, began setting up a portable sonar fence to protect the dock area. The team later captured Sawyer and took him to Widmore aboard the submarine. The two struck a deal: if Sawyer led the Man in Black into a trap, Widmore would transport him and his friends safely off the Island. (6x08)
Sawyer later decided to capture Widmore's submarine as the vehicle to get him and other survivors off the Island. (6x13) However, the Man in Black attempted to sabotage his plan by placing a bomb aboard the sub. Sayid took the bomb away from the group and it blew a hole in the sub, killing him, and filling it with water until it sunk to the bottom of the ocean. Sun and Jin drowned. (6x14)
The submarine type resembles the 1980s Japanese Yūshio class submarine, which was widely decommissioned in the early years of the 21st century.