The 13th Floor Elevator is used mostly by Thaddeus Valentine for archaeological expeditions and other adventures. He used it to travel to The Dead Continent to retreive pieces of MEDUSA. Valentine also used the airship to travel to Pandora Shaw and steal the MEDUSA computer core from her.
At Batmunkh Gompa, when Valentine is fighting Anna Fang, Anna is distracted by the lights of the 13th Floor Elevator. Thaddeus takes this to his advantage and grabs Anna's sword and drives it through her neck, killing her. Above London, Tom Natsworthy battles the 13th Floor Elevator. However all the missiles are effectless against The 13th Floor Elevator's armour. He then realises that while the envelope is armoured, the cabin is not. He fires a missile at the cabin. The 13th Floor Elevator explodes and falls down towards London, Pewsey and Gench are screaming inside. The burning wreck of the ruined airship lands on Bevis Pod, killing him instantly.
Afterwards, Tom is deeply ashamed that he shot down the 13th Floor Elevator and remembers witnessing the two pilots burning alive inside the cabin as it fell. Because of that, he disables the Jenny Haniver's missile pods, as he doesn't want it to be used for violence again.