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In an e-mail to the Associated Press, machinist mate John Krzemien said that “morale has definitely taken a hit” since Capt. Honors was relieved.

“They took the one captain that could rally this much support and replaced him because of civilian opinions,” he wrote. “None of us think it’s right.”

But along Pier 12 in the hours before the Enterprise’s deployment, family and crew said they had confidence in their new commander.

“They respect him just as much,” said Tonya Hudson, who saw off her husband, Lt. Jason Hudson, with their three children. They had breakfast on the Enterprise, where many crew members had spent the night. “As far as I can tell, I think morale is high and they’re ready to go.”

Her sea bag slung over her shoulder, culinary specialist Melissa Williams said she wasn’t reflecting on the past, just her first deployment.

“I’m very honored to do it,” she said. “Morale is good.”

The Enterprise’s deployment without Capt. Honors underscored an abrupt change of fortune for the boyish-looking officer, a U.S. Naval Academy graduate who became a Top Gun pilot. Capt. Honors flew 85 combat missions in three theaters, landing on 15 different carriers. He has since been reassigned to an administrative job.

The Virginian-Pilot of Norfolk first reported the existence of the videos nearly two weeks ago and posted excerpts. The Navy said the videos were intended merely as humorous skits and stopped airing them immediately after other senior officers became aware of them.

No leaders in senior posts at the Pentagon and in the Navy could explain why Capt. Honors was promoted after they became aware of the videos.

The probe is looking into actions by Capt. Honors and also into who among his superiors knew of the videos and what they did about them at the time. Adm. Rice commanded the Enterprise from December 2004 to May 2007; Rear Adm. Ron Horton commanded the ship from mid-May 2007 to May 2010. Adm. Horton is still on active duty and therefore  remains available to cooperate with the investigation.

The Enterprise led a carrier strike group that includes an air wing, four destroyers and a supply ship. A total of 6,000 sailors and Marines are part of the deployment.

• Pauline Jelinek reported from Washington.