Lonsdale's next command on 1 November 1938 was Seal, which he commissioned in May 1939. The ship's company "one of the biggest collections of scallywags that the Submarine Service ever put together" were confronted by a slight quiet man who was considered "Too much of a gentleman to be a good submarine captain". However in a very short time, by no perceptible means, Lonsdale had gained the complete respect, faith and confidence of his crew. After missions in the China Sea, at Aden, on the North Atlantic and North Sea Patrol, the submarine’s last mission was to cross the Skagerrak and lay a minefield in the Kattegat - an almost impossible task for a submarine as large as Seal. Lonsdale's superior, Captain Bethall, failed to persuade Admiral Horton to reconsider his orders and the ship sailed on 29 April. She was held in check by German anti-submarine trawlers in the area, but managed to lay her mines. She was hunted by two German search flotillas and took evasive action to escape the area when she went into an uncharted minefield. A German mine exploded while she was on the sea bed, damaging her stern and filling her hull. The attempt to resurface had to wait several hours until it was dark. However, in spite of three attempts, the damaged submarine failed to lift from the seabed and air quality deteriorated significantly. Throughout the incident the crew were impressed by the quiet resolution and faith of their captain. As a devout Christian, Lonsdale summoned his ship's company to prayer, and led them in the Lord's Prayer. After taking several last desperate measures, he made another attempt and the submarine finally lifted. Once on the surface he tried to make for the nearby Swedish coast and the crew destroyed the secret Asdic equipment and confidential papers. The stricken submarine was spotted and attacked by enemy aircraft. Lonsdale sent his crew below, and under intense fire tried to hold the aircraft off with Lewis guns until these jammed. The submarine was without motive power, unable to dive and without any defences and there was no realistic alternative but to surrender. Various action were taken towards scuttling the boat but it managed to stay afloat.
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