Pipes, tanks and other equipment rust in the humid Southern air. Leaky roofs leave puddles on factory floors. Abandoned buildings are scattered across an 800-acre site contaminated with hundreds of tons of mercury..

If this were a factory making cars in Detroit or steel in Pennsylvania, it would have long ago been shuttered.

But this is the Y-12 National Security Complex, a linchpin of the Energy Department’s nuclear weapons complex, responsible for making thermonuclear assemblies for hydrogen bombs.

The 1940s-era plant is part of a weapons program that has become increasingly costly to operate because of aging equipment, deteriorating facilities and soaring overhead costs. At its root, it is bloated and mismanaged, say former Energy Department officials, outside experts and members of Congress.

The nation’s nuclear weapons stockpile has shrunk by 85% since its Cold War peak half a century ago, but the Energy Department is spending nine times more on each weapon that remains. The nuclear arsenal will cost $8.3 billion this fiscal year, up 30% over the last decade.

The source of some of those costs: skyrocketing profits for contractors, increased security costs for vulnerable facilities and massive investments in projects that were later canceled or postponed.

“We are not getting enough for what we are spending, and we are spending more than what we need,” said Roger Logan, a senior nuclear scientist who retired in 2007 from Lawrence Livermore National Laboratory. “The whole system has failed us.”

The Defense Department’s fleet of submarines, bombers and land-based missiles is also facing obsolescence and will have to be replaced over the next two decades, raising the prospect of further multibillion-dollar cost escalations.

Now the Obama administration is moving forward with a plan to modernize the strategic weapons system over the next decade, an effort the Congressional Budget Office estimates will cost $355 billion. That comes as the Pentagon is under pressure to reduce its budget, and outside experts warn that the modernization could reach $1 trillion over the next 30 years.

“Simply stated, there is no plan for success with available resources,” said Norman Augustine, a former Pentagon and defense industry official who is leading a review of the Energy Department’s bomb program.

U.S. nuclear weapons strategy rests on a triad of delivery systems — bombers, submarines and land-based missiles — developed early in the Cold War to deliver warheads anywhere in the world.

The three legs of the triad were designed to ensure that even in a massive surprise attack, at least one leg would survive to deliver a retaliatory strike.

Today, elements of the systems are virtual museum pieces. An example is the B-52. One of the massive gray bombers recently sitting on a tarmac at the Global Strike Command at Barksdale Air Force Base in Louisiana rolled off Boeing Co.’s assembly line in 1960 — during the Eisenhower administration.

Under current plans, B-52s will probably fly another 26 years. By the time the bomber retires, it will be 80 years old — older than any strike aircraft ever flown in military service.

The other legs of the nuclear triad are 450 1960s-era Minuteman III missiles based in silos in Wyoming, Montana and Nebraska, and 14 Ohio-class submarines from the 1980s that are also nearing the end of the design life of their nuclear propulsion systems.

The nuclear warheads that these vehicles carry are maintained at the legacy sites of the Manhattan Project. Although it is significantly smaller than in its Cold War heyday, the Energy Department industrial complex stretches from South Carolina to California with more than 40,000 employees.

The department has three scientific design laboratories, a site for underground experiments the size of Rhode Island and an assembly factory on the flatlands of West Texas, despite the fact the government hasn’t designed, built or tested a new nuclear warhead in decades.

When the U.S. stockpile reached its peak in 1967 with 31,255 warheads and bombs, it cost $7 billion annually in today’s dollars to build and maintain nuclear weapons.

In that year, the government had seven reactors humming to make plutonium; it built submarine reactors, refined large quantities of plutonium and uranium and manufactured new weapons. Almost once a week, it set off a bomb underground in Nevada.

Today, it does none of those things, but simply maintains the existing 4,804 weapons at $1.3 billion more than in 1967. And the costs would be even higher if items such as submarine reactors, included in the 1967 budget, were added.

Don Cook, chief of the nation’s nuclear weapons program for the Energy Department, argued that the size of the stockpile doesn’t matter, because the facilities still have to have capability and special machines to repair even small numbers of weapons.

“You would think the saving grace would be having smaller numbers of weapons, so somehow it must be cheaper, but it doesn’t work that way,” Cook said.

Critics sharply dispute that assertion, saying the department’s capacity is beyond its needs, its vast complex is a political pork barrel, and its operations are hindered by mismanagement.

Profits paid to the contractors that run the system have tripled since 2006 to $312 million, The Times found.

The eight major nuclear weapon labs and production sites are run by a network of joint ventures and private companies, including the University of California, Bechtel Corp., Northrop Grumman Corp., Honeywell International Inc. and Lockheed Martin Corp.

The increases came after a series of embarrassing security lapses at Los Alamos National Laboratory while it was managed by the University of California. The lapses led to a movement to pay more and demand far stricter security.

Cook said the agency knew it would have to pay more to attract top-tier defense contractors. “Part of the deal was profit,” he said.

As a result, profits paid to the new consortium hired to run the Los Alamos lab jumped tenfold to $59 million in 2013. At Lawrence Livermore National Laboratory, which is now run by the University of California and San Francisco-based Bechtel, among others, profits grew from $4 million to $41 million.

Costs for security at the labs since 2003 have doubled to $665 million annually in the last decade, a response to Sept. 11. The department also spends more than $100 million a year on cyber security.

Another major cost is maintaining parts for the nation’s nuclear arsenal. Of 70,000 nuclear weapons that the U.S. built, only about 4,800 remain in service. But the government must still maintain a costly inventory of old parts.

Those parts, as well as some retired parts that are too sensitive or toxic for disposal, all have to be guarded in high-security warehouses, said Philip Coyle, former deputy director of the Lawrence Livermore National Laboratory and more recently scientific advisor to the Obama administration.

At a Texas warehouse, congressional investigators this year found a stash of 3 million parts, about half of them common screws, nuts and bolts that did not appear to need any special security measures.

In 2010, the Energy Department opened a $549-million warehouse at Y-12 for thousands of parts. Among the parts are pieces of a megaton-sized weapon that is stored in case Earth has to be defended from an inbound asteroid, according to a report by the Government Accountability Office.

The $355-billion modernization plan being championed by the Obama administration would upgrade weapon production facilities, refurbish warheads and build new submarines, bombers and ground-based missiles.

The Air Force wants $91 billion to design and build 80 to 100 bombers to replace B-52 and B-2 bombers. The Navy plans to replace its fleet of 14 missile submarines with 12 new boats, along with new missiles, costing about $60 billion. The Air Force would get new land-based missiles and a command-control system for the underground silos at a yet unspecified cost.

“If modernization isn’t done properly, the perception of U.S. strength is at risk — and by extension our national security is at risk,” said Norton A. Schwartz, a retired four-star general who served as Air Force chief of staff.

So far, Congress has set aside only a small fraction of that money. The Energy Department has made several attempts to replace outdated facilities, but the efforts have collapsed.

This year, the department shelved plans for a new plant in South Carolina that would have converted surplus plutonium to commercial reactor fuel. Nearly $4 billion was spent before the project was deemed too expensive.

The department also halted a new plutonium manufacturing plant in New Mexico when the cost shot up sixfold to $5.8 billion.

At the Y-12 National Security Complex, officials put on hold plans to replace the main production facility, a uranium foundry known as Building 9212 that was built during World War II. The Defense Nuclear Facilities Safety Board, a federal oversight panel, has warned that an earthquake could cause the building to collapse, trigger a fire and release uranium into the environment.

The project to replace it was stopped after costs rose from $600 million to between $12 billion and $19 billion, after $500 million was spent.