The somber deactivation ceremony at Portsmouth Naval Shipyard marked the end of the sub’s nearly 24 years of active service.

Rear Adm. Ken Perry, commander of the submarine Group Two in Groton, Conn., where the sub was based, acknowledged the seriousness of the event, but told the crowd they were there to celebrate the submarine and its crew’s achievements.

“This is a tribute. This is a celebration of the ship’s performance and the superb contributions to the nation’s defense and this is how we’re going to treat it. So I expect to see some smiles out there,” he said.

Cmdr. Rolf Spelker, the sub’s current commander, said he came to Portsmouth thinking his assignment was to prepare the ship for service. He said he and crew members are disappointed that instead, their duty was to help inactivate the vessel.

“They are no doubt disappointed and saddened that they can’t take her out to sea,” Spelker said.

Perry praised the ship’s performance over more than a dozen deployments that included clandestine undersea warfare missions and back-to-back deployments in which it fired cruise missiles in Iraq and in Serbia, cementing its reputation and nickname as “Big Gun.” It should have had about 10 years of service left.

After the fire, the Navy originally intended to repair the Miami with a goal of returning it to service in 2015. But it decided to scrap the submarine after estimated repair costs grew substantially above a $450 million estimate.

Instead, shipyard workers will remove fuel from the nuclear reactor and take it to a repository in Idaho. They will make enough repairs so that the submarine can be towed to Puget Sound Naval Shipyard in Washington state, where it will be cut up for scrap. The estimated cost of the inactivation is $54 million.

It was a bitter loss because of the way the submarine was damaged, at the hands of a shipyard worker who set a fire to the vessel in May 2012 while the submarine was undergoing a 20-month overhaul.

Seeking an excuse to leave work early, Casey James Fury set fire to a box of rags on a bunk, and the blaze quickly spread throughout the forward compartments of the Los Angeles-class submarine. Fury pleaded guilty and is serving a sentence of more than 17 years in federal prison.

It took 12 hours and the efforts of more than 100 firefighters to save the vessel.

The fire severely damaged living quarters, the command and control center and a torpedo room, but it did not reach the nuclear propulsion components at the rear of the sub. Seven people were hurt dousing the fire, the Navy said.

The Navy launched a series of investigations after the fire that led to recommendations, including installation of temporary automatic fire detection systems while submarines are in dry dock.