The S.S. Libra is a ship that was abducted and subsequently left destroyed in the middle of the desert, just south of the Cipher Key Lair and southwest of Eclo Canyon. It is surrounded by large amounts of unstable sand, making it impossible for Michael to make it at first until he is able to upgrade his scooter so it can hover.
When the ship was dropped in the desert, Gorigan and his Cipher Peons stole every Pokemon off of the ship, except for a Bonsly that they missed, and took them to the Cipher Key Lair to turn them into Shadow Pokemon. According to Lovrina, they had intended to bring the ship to the Cipher Key Lair, but because of some issues with shadow Lugia, it fell in the middle of desert and Cipher had to locate it so they could take the Pokemon from it.
According to the ONBS, the two crewmen that were thrown overboard when the ship was stolen had not been not found and as the game progresses it is unknown whether the crew members were ever found.
The ship now acts as shelter for a man living inside of it and the Bonsly owned by the man at the ONBS. When Michael goes to find the Bonsly, it is scared away by his P★DA. During this visit, he also encounters Gorigan for the first time and fights one of his Cipher Peons. As he is exiting, he comes across encounters two Snagem goons who knock him out and steal his Snag Machine.
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