Bolts can be used to repair the jet ski on the H.M.S. Orca.
Bolts are also used to make the Crossbow Body for the "Zip it Up" escape in Rattlesnake Springs.
It can be found in desks on H.M.S. Orca and Rattlesnake Springs. In U.S.S. Anomaly, bolts can be looted from guard inventory.