While conducting her 5th war patrol on November 16, 1942, under the command of Lt Commander Kenneth C Hurd, the seal had a "bad moment" and was run down by a Japanese merchant ship. Seal survived but it is unknown if the Japanese ship sank. She was at the lest badly damaged. According to her war report, "...quantities of uncooked rice and beans, unlike those used on the submarine, were found between the wooden deck pieces of the cigarette deck, on the bridge, and caught in the bathythermograph. The periscope shears yielded "...a good sample of Japanese bottom paint." "

Her War Damage Report Summery reads: "While at 61 foot depth and only twelve seconds after firing torpedoes at a Japanese freighter, Seal was run down by a second Japanese cargo ship which passed directly overhead and damaged the periscopes, radar, and their supporting shears. Boat rose from 61 feet to 55 feet due to suction effect and hung there for nearly a minute before starting down. No. 2 periscope, which was fully extended, was bent nearly horizontal at top of shears. SD radar mast was also bent over in same direction. No. 1 periscope could not be operated due to misalignment of upper bearings. No. 2 periscope housing was broken off level with top of housing for No. 1 periscope. No other damage occurred. Patrol was terminated."

With this event the Japanese knew the submarine was there and began a search and as the Seal leveled off at 250 feet depth charges began dropping from the escort ships. Soon breaking up noises were heard but if from the damaged cargo ship sinking is unknown. After four hours at depth and things quieting down, the Japanese perhaps thinking the Seal sunk from the collision, the Seal surfaced and departed the area and began assessing her damages. After the wars end it was reported that the torpedoes fired just before the collision resulted in; "...confirmed the sinking of the 3,500-ton freighter BOSTON MARU by an American submarine on that date in that location."

A photo taken in the ward room of the USS Seal SS 183. The date of the photo is not known for certain but it can be place between 1943 and mid 1944. The man in the middle is the Seal Commanding Officer, Lt.Commander Harry B. Dodge along with other unidentified officers from the Seal. Dodge is sitting in the Captains chair which was located at the aft end of the ward room table. The most senior officers sat near the Captain and least senior sat at the opposite or forward end of the table.

The cabinetry behind Dodge held, as seen, books of all kinds from recreational to technical books. The cabinet below had drawers that held charts and much of the ward room silver service and dishes and serving plates and bowls. A large fan can be seen above Dodges' head

The photo was taken after a meal had been served and before the Steward had cleared away the dirty dishes. An ashtray can be seen next to Dodges right hand. The man to the right of Dodge could possibly be the Seals' Executive Officer, Lt. Robert Duryea. He is sitting in the seat usually occupied by a ships Executive Officer. Especially if this photo was taken right after a meal the officers would be sitting in their allocated seating and he is wearing Lieutenants Bars.

Following Navy protocol, the officer to Dodges left would be the Engineering Officer and the man closest to the camera on Dodges right would be the Operation/Navigation Officer. The man barely seen at the far right of the photo would probably be the Weapons Officer. Photo could possibly be taken by the Supply Officer as it is taken from a seated position. Supply Officers were the least senior of officers and sat at the far end opposite the Captain. It possibly could have been taken by a Steward.