YOKOSUKA NAVAL BASE, Japan — The guided-missile cruisers USS Antietam and USS Cowpens swapped crews Tuesday in a move that Navy officials say will give its only Asia-based fleet a more sophisticated missile-defense system.

The Antietam will remain based in Yokosuka, while Cowpens will sail back to San Diego and face a far less certain future.

Although the two Ticonderoga-class ships are both about 20 years old and look roughly the same on the outside, budgetary realities have turned them into vastly different ships.

Antietam recently underwent a thorough midlife overhaul that gives the cruiser more capability against ballistic missiles and more efficient ways to attack. Below decks, old standbys such as boilers have been removed and replaced with all-electronic systems, Navy officials said.

“It is a game changer in terms of air defense, and command and control,” Capt. Thomas Disy, Antietam’s new commander, said following the hull swap.

Cowpens was one of seven cruisers slated by Navy leaders for decommissioning in 2012, and one of four that was supposed to leave the fleet entirely in 2013. Vice Adm. Bill Burke, at the time the Navy’s head of readiness logistics, told Congress last year that modernizing all seven cruisers would have cost $5 billion.

However, Congress blocked the decommissioning under the rationale that it would cost more to build new ships than to fix older ones. Rep. Randy Forbes, R-Va., noted that while the fleet’s ship numbers are slated to shrink over the next decade, its workload shows no sign of decreasing.

The cruisers’ scheduled demise also meant that maintenance funding wasn’t planned for the ships, further clouding their long-term future.

In the short term, Navy officials said Tuesday that Cowpens remains operational and would be available for deployment when it joins the fleet in San Diego.

Both crews have been preparing for months to complete the hull swap, said Rear Adm. Mark Montgomery, commander of the Yokosuka-based Commander Task Force 70. Montgomery likened getting the two ships operating together — they are literally docked side-by-side and connected by a gangplank — to the completion of the first half of a football game.

“This is like Beyoncé and Destiny’s Child up here,” Montgomery said, in a reference to Sunday’s Super Bowl halftime show at the hull swap ceremony.

During the proverbial second half, Montgomery said, both crews get certified in Japan as safe operators of their new ships, before either cruiser redeploys.

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