Despite a recent repair and upgrade, Dolphin was decommissioned on 15 January 2007 and stricken from the Naval Vessel Register on the same date.

[citation needed] Employed in both civilian and Navy activities, Dolphin was equipped with an extensive instrumentation suite that supported missions such as acoustic deep-water and littoral research, near-bottom and ocean surveys, weapons launches, sensor trials, and engineering evaluations.

She has internal and external mounting points, multiple electronic hull connectors, and up to 10 equipment racks for project use.

][citation needed] On 21 May 2002, around 23:30 PDT, while operating roughly 100 miles (160 km) off the coast of San Diego, California, Dolphin was cruising on the surface, recharging her batteries, when a torpedo shield door gasket failed, and the boat began to flood.

Due to high winds and 10-to-11-foot (3.0 to 3.4 m) swells in the ocean, around 75 tons of seawater entered the ship, an amount perilously close to the boat's reserve buoyancy.

The Oceanographic Research ship William McGaw was operating in the vicinity, and immediately responded to Kelety's call for assistance.

USS Thach also came alongside Dolphin and rescued several crewman from the water, but the seas were too rough for full recovery or towing operations.

Submarine Support Vessel Kellie Chouest got underway from San Diego early on 22 May to assist in recovery.

[citation needed] In mid-2006, the Navy decided to retire Dolphin, citing the $18 million her operations cost annually.

Dolphin was officially transferred to the San Diego Maritime Museum in September 2008, to become the eighth vessel in their floating collection.