After the second penetration of the Antarctic, the squadron rendezvoused in New Zealand in April 1840 to survey Pacific islands northward toward the Hawaiians, where the ships were repaired late in the year. Flying Fish sailed with to resurvey some of the Samoan, Ellice, Kingsmill, and Pescadore Islands before joining the main body of the squadron on the northwest coast of America in July 1841. Flying Fish made surveys in the Columbia River and around Vancouver, then proceeded to San Francisco, from which the squadron sailed 1 November for the south Pacific. Arriving in the Philippines in mid-January 1842 Flying Fish and the other ships separated to cruise the Sulu Seas, then make a planned rendezvous at Singapore in February.
