In 1998, her sister-ship Sirius was torpedoed by the submarine Spartan as a target-ship, making Scylla the last remaining Leander left in the UK. She lay in a state of disrepair for ten years until the 27 March 2004, when she was sunk off Whitsand Bay, Cornwall to form an artificial reef; the first of its kind in Europe. Her last CO, Captain Mike Booth, and former crew members were present during the sinking. Daniel Green, a keen diver and student of a local school who won a BBC competition to sink the ship, and David Bellamy OBE, had the liberty of pressing the plunger to detonate the ship.
A lot of work was done to ensure the ship was safe and easy to explore inside, such as cleaning the oil from the hull to prevent marine contamination, and as expected, she has become a very popular dive site, situated some 40 minutes by boat from Plymouth. The bridge, rear helicopter bay and deck and the side passages are all visible. Additionally there are penetration dives possible, which have all been made safe for diving.
In August 2006 a team of Marine biologists from the National Marine Aquarium and simulation experts from the University of Birmingham conducted a dive with a Videoray ROV onto the wreck of the Scylla. The dive lasted just over an hour, with the main purpose being to investigate the growth of marine life on the wreck and to collect data for a unique artificial life and serious game project, the Virtual Scylla addressing interactive educational tools for teaching climate change and ocean awareness.
The sinking of HMS Scylla has benefitted Devon and Cornwall's economy, with a large increase in visitor numbers to the National Marine Aquarium and local diving schools reporting a large increase in divers wanting to experience the wreck.