Unlike the rest of the Trafalgar-class boats that followed, she was not launched with a pump-jet propulsion system, but with a conventional 7-bladed propeller.

She was welcomed back by Admiral Sir Alan West, Commander-in-Chief of the fleet and it emerged she was the first Royal Navy submarine to launch Tomahawk cruise missiles against Afghanistan.

[7] In November 2002, Trafalgar again ran aground close to the Isle of Skye, causing £5 million worth of damage to her hull and injuring three sailors.

She was travelling 50 metres below the surface at more than 14 knots when Lieutenant-Commander Tim Green, a student in the "Perisher" course for new submarine commanders, ordered a course change that took her onto the rocks at Fladda-chuain, a small but well-charted islet.

[8] In May 2008 it was reported that the crash was caused by the chart being used in the exercise being covered with tracing paper, to prevent students marking it.