Capt. Owen Honors wasand assigned to onshore administrative duties. His naval career is likely over. A top admiral says he's "lost confidence" in Honors' ability to "lead effectively."
But no leaders in senior posts at the Pentagon and in the Navy could explain why, if Honors' conduct was so questionable, he was promoted after the videos aired in 2006 and 2007 and reprimanded only after the offensive videos became public.
Senior military officials said they were trying to determine who among Navy leaders knew about the videos when they were shown repeatedly to thousands of crew members aboard the nuclear-powered aircraft carrier.
An investigation by U.S. Fleet Forces Command also is seeking to determine whether Honors was reprimanded at the time.
The episode has raised serious questions about whether military leaders can behave badly so long as the public doesn't find out.
"He showed bad judgment and he embarrassed the Navy. Those are things that are going to be hard for the Navy to ignore or to forgive," said Stephen Saltzburg, the general counsel of the National Institute of Military Justice and a law professor at George Washington University.
Just two days after the videos were shown repeatedly on television, the Navy called a news conference Tuesday in Norfolk to announce that Honors was stepping down as ship commander and being reassigned to administrative duties ashore.
"After personally reviewing the videos created while serving as executive officer, I have lost confidence in Capt. Honors' ability to lead effectively," said Adm. John Harvey, head of U.S. Fleet Forces Command. Harvey declined to answer questions from reporters.
The Pentagon said the disciplinary system isn't foolproof but generally works.
"There are always going to be people do things they shouldn't," said Marine Corps Col. Dave Lapan, a Pentagon spokesman. "They will be held accountable."
Yet Honors was set to deploy with the USS Enterprise this month as the ship's commander when The Virginian-Pilot in Norfolk obtained videos he made three and four years ago as the carrier's executive officer. Honors, who took command of the ship in May, appears in the videos using gay slurs, simulating masturbation and staging suggestive shower scenes.
One video also briefly included Glenn Close, which the actress called "deeply offensive and insulting." Close said in a statement that she appeared in a clip after a "seemingly innocent request" made during a visit to the USS Enterprise more than four years ago.
While many sailors aboard the ship at the time have defended Honors on Facebook postings - contending he was simply providing a much-needed morale boost during long deployments at sea - senior military officials interviewed by The Associated Press said the videos were extreme and showed a disturbing lack of judgment.
According to the Pentagon, Defense Secretary Robert Gates and Chairman of the Joint Chiefs of Staff Adm. Mike Mullen weren't aware of the videos until this week. They were said to have left any disciplinary action up to the Navy.
Tuesday's removal from command effectively ends Capt. Owen Honors' Navy career, and many expect Honors to retire, CBS News Correspondent Bob Orr reports.
Capt. Dee Mewbourne has been named the new commander of the USS Enterprise. He is a former commander of the carrier USS Dwight D. Eisenhower.