Getting stuck in the mud on its first attempt to leave Manhattan was not the last or the least of the troubles that the aircraft carrier Intrepid has encountered in the past 18 months.

The military museum the ship houses was at risk of going out of business last year, as the costs of overhauling the carrier and rebuilding its home pier spiraled past $100 million, almost double the original estimate, said Bill White, president of the Intrepid Sea, Air & Space Museum. To keep the work going and to stay on schedule to reopen this fall, the museum’s directors borrowed against the museum’s $15 million endowment, a move they had promised never to make, Mr. White said.

“This museum and this whole project was in danger of shutting down,” Mr. White said. “If we hadn’t taken this drastic measure to use the endowment, which I consider sacred, for this purpose, there would be no more Intrepid — unless someone was willing to write a check for 15, 20 million bucks.”