Kittery, Maine — While the ceremony Friday honoring the USS Miami celebrated the many accomplishments of the submarine and its sailors, the commanding officer said after the event that he and the crew are disappointed and saddened to have to say goodbye early.

The crew, Cmdr. Rolf Spelker said, has "gone through the tidal wave of emotions, from the disaster to fixing the ship to now inactivating the ship."

"They realize it was a fiscal decision made by Navy leadership, and given these financial times, it only made sense," Spelker said. "They're dealing with that. They're doing their job."

More than 80 members of the Miami's crew have served on other ships.

The Navy held Friday's decommissioning ceremony for the Groton-based Los Angeles-class submarine in an auditorium at the Portsmouth Naval Shipyard. The Miami (SSN 755) was at the shipyard for a 20-month overhaul when a civilian worker set a fire aboard the vessel on May 23, 2012. The Navy initially said it would repair the ship but later decided to scrap it after nearly 24 years of active service in the fleet because of rising cost estimates and fiscal constraints.

The Miami had 10 years and five deployments left in its service life.

Rear Adm. Kenneth M. Perry, the commander of Submarine Group Two, said in an interview after the ceremony that while it was a tough call, inactivating the Miami was the prudent and right decision. The loss puts additional stress on the submarine force, he said, "but we're managing it."

Perry also emphasized that the Miami is still "delivering for our force" because some of its parts have been installed on other submarines. The Miami's propeller shaft went to the USS Topeka.

Removing the parts was meaningful work the crew could do while waiting to inactivate the ship, Spelker said. But Perry added, "Let's face it, we don't join the Navy to go give our parts away to other submarines."

"They're doing what they need to do to support the submarine force and other ships," Perry said. "But clearly if I'm a member of a crew, I'd rather be refurbishing, preparing, lining up that gear for my own operations."

During the ceremony, Perry focused his remarks on the life of the Miami, not its end. He said the event was a tribute to the ship's performance over the years "and that's how we're going to treat it."

"I expect to see a few smiles out there," he told the audience.

In 1994, the Miami was the first nuclear-powered submarine to pass through the Suez Canal, Perry said. In the late 1990s, it launched Tomahawk cruise-missile strikes during Operation Desert Fox in Iraq and Operation Allied Force in Kosovo and became the first submarine since World War II to fire ordnance during combat operations in two different theaters. That, Perry said, earned Miami the nickname "The Big Gun."

Perry told the sailors in the audience that they will carry the submarine's legacy forward. "Miami's reputation for excellence will endure through you and the sailors you lead," he said.

Retired Capt. Thomas Mader, the Miami's first commanding officer, told the audience about the day the boat was launched at Electric Boat in Groton as the most technologically advanced submarine of its time. He said Friday's ceremony was a celebration of the generation of submariners who dedicated themselves to the Miami's missions.

Mader, who served as skipper of the submarine from 1987 to 1990, was one of several former Miami commanding officers who attended the ceremony. He said it was an honor and pleasure to bid a fond farewell to the Miami and he told the current crew that they have "weathered some uncertain times," and that they have proven their mettle by rising to the challenge.

At the end of the ceremony, the sailors stood and each department reported that it was ready to decommission the ship. The order was given to strike the commissioning pennant and lower the ensign. Both were presented to Spelker, and the audience applauded as the crew left the auditorium.

The Miami was built at Electric Boat in Groton and commissioned June 30, 1990, as the Navy's 44th Los Angeles-class submarine. During more than a dozen deployments over the past two decades, it operated in the North Atlantic, the Mediterranean, the Red Sea, the Adriatic Sea and the Persian Gulf.

Casey James Fury, a civilian painter and sandblaster, was sentenced to more than 17 years in federal prison last year after he pleaded guilty to setting fire to rags aboard the Miami. He told authorities he suffered from anxiety and wanted to leave work. Seven people were injured fighting the blaze, which burned for 12 hours.

After the fire, the discovery of additional damage raised repair costs from an estimated $450 million to $700 million. The estimated cost for the inactivation is $54 million. The Miami will be towed to the Puget Sound Naval Shipyard next spring. Its crew members will be reassigned to other units by December.

j.mcdermott@theday.com