Based on a forensic analysis going back months, it appears the hackers broke into The Times computers on Sept. 13, when the reporting for the Wen articles was nearing completion. They set up at least three back doors into users’ machines that they used as a digital base camp. From there they snooped around The Times’s systems for at least two weeks before they identified the domain controller that contains user names and hashed, or scrambled, passwords for every Times employee. While hashes make hackers’ break-ins more difficult, hashed passwords can easily be cracked using so-called rainbow tables — readily available databases of hash values for nearly every alphanumeric character combination, up to a certain length. Some hacker Web sites publish as many as 50 billion hash values. Investigators found evidence that the attackers cracked the passwords and used them to gain access to a number of computers. They created custom software that allowed them to search for and grab Mr. Barboza’s and Mr. Yardley’s e-mails and documents from a Times e-mail server.