In late 1870, she was selected for service with the Hall scientific expedition, led by Charles Francis Hall, and was sent to the Washington Navy Yard for refitting. Renamed USS Polaris in early-1871, she arrived at the New York Navy Yard on June 9 to complete loading of stores and provisions for the expedition. She set sail in July 1871.

Aiming for the North Pole, she reached 82° 29′N latitude, then the furthest point north reached by a vessel. Polaris was caught in the ice on the homeward voyage in October 1872, and carried for some distance before being crushed. Her crew was subsequently rescued, including a party of 18 people led by William F. C. Nindemann, who had debarked to land provisions after the hull of the Polaris had begun to leak, only to have the section of the ice floe they were on break away from the section holding the Polaris.

The lost party floated for 196 days and were subsequently rescued separately from the vessel.

A naval board of inquiry investigated Charles Hall's death, but no charges were ever laid. However, an exhumation of his body in 1968 revealed he had ingested a large quantity of arsenic in the last two weeks of his life. Coupled with recently discovered affectionate letters written by both Hall and Bessels to Vinnie Ream, a young sculptor they met in New York while waiting for Polaris to be outfitted, suggests Bessels had a motive, besides the means, to kill Hall.