Following the establishment of their website, The New York Times retained its journalistic hesitancy from executive editor Joseph Lelyveld's refusal of publishing an article on the Clinton–Lewinsky scandal from Drudge Report. Editors conflicted with print editors on several occasions, including wrongfully naming security guard Richard Jewell as a suspect in the Centennial Olympic Park bombing and covering the death of Diana, Princess of Wales in greater detail than the print edition. The New York Times Electronic Media Company was adversely affected by the dot-com crash. The Times extensively covered the September 11 attacks. The following day's print issue contained sixty-six articles, which included the work of over three hundred dispatched reporters. Journalist Judith Miller was the recipient of a package containing a white powder during the 2001 anthrax attacks, furthering anxiety within The New York Times. In September 2002, Miller and military correspondent Michael R. Gordon wrote an article claiming Iraq had purchased aluminum tubes. The article was cited by then-president George W. Bush to claim that Iraq was constructing weapons of mass destruction; the theoretical use of aluminum tubes to produce nuclear material was subject of debate. In March 2003, the United States invaded Iraq, beginning the Iraq War.
An article in December 2005 disclosing warrantless surveillance by the National Security Agency contributed to further criticism from the George W. Bush administration and the Senate's refusal to renew the Patriot Act. In the Plame affair, a Central Intelligence Agency inquiry found that Miller had become aware of Valerie Plame's identity through then-vice president Dick Cheney's chief of staff Scooter Libby, resulting in Miller's resignation.
During the Great Recession, The New York Times suffered significant fiscal difficulties as a consequence of the 2007 subprime mortgage crisis and a decline in classified advertising. Exacerbated by Rupert Murdoch's revitalization of The Wall Street Journal through his acquisition of Dow Jones & Company, The New York Times Company started enacting measures to reduce the newsroom budget. The company was forced to borrow million () from Mexican business oligarch Carlos Slim and fired over one hundred employees by 2010. nytimes.com's coverage of the Eliot Spitzer prostitution scandal, resulting in the resignation of then-New York governor Eliot Spitzer, furthered the legitimacy of the website as a journalistic medium. The Timess economic downturn renewed discussions of an online paywall; The New York Times implemented a paywall in March 2011. Abramson succeeded Keller, continuing her characteristic investigations into corporate and government malfeasance into the Timess coverage. Following conflicts with newly-appointed chief executive Mark Thompson's ambitions, Abramson was dismissed by Sulzberger Jr., who named Dean Baquet as her replacement.
Leading up to the 2016 presidential election, The New York Times elevated the Hillary Clinton email controversy and the Uranium One controversy; national security correspondent Michael S. Schmidt initially wrote an article in March 2015 stating that Hillary Clinton had used a private email server as secretary of state. Donald Trump's upset victory contributed to an increase in subscriptions to the Times. The New York Times experienced unprecedented indignation from Trump, who referred to publications such as the Times as "enemies of the people" at the Conservative Political Action Conference and tweeting his disdain for the newspaper and CNN. In October 2017, The New York Times published an article by journalists Jodi Kantor and Megan Twohey alleging that dozens of women had accused film producer and The Weinstein Company co-chairman Harvey Weinstein of sexual misconduct. The investigation resulted in Weinstein's resignation and conviction, precipitated the Weinstein effect, and served as a catalyst for the #MeToo movement. The New York Times Company vacated the public editor position and eliminated the copy desk in November. Sulzberger Jr. announced his resignation in December 2017, appointing his son, A. G. Sulzberger, as publisher.
Trump's relationship—equally diplomatic and negative—marked Sulzberger's tenure. In September 2018, The New York Times published "I Am Part of the Resistance Inside the Trump Administration", an anonymous essay by a self-described Trump administration official later revealed to be Department of Homeland Security chief of staff Miles Taylor. The animosity—which extended to nearly three hundred instances of Trump disparaging the Times by May 2019—culminated in Trump informing federal agencies to cancel their subscriptions to The New York Times and The Washington Post in October 2019. Trump's tax returns have been the subject of three separate investigations. During the COVID-19 pandemic, the Times began implementing data services and graphs. On May 23, 2020, The New York Timess front page solely featured U.S. Deaths Near 100,000, An Incalculable Loss, a subset of the 100,000 people in the United States who died of COVID-19, the first time that the Timess front page lacked images since they were introduced. Since 2020, The New York Times has focused on broader diversification, developing online games and producing television series. The New York Times Company acquired The Athletic in January 2022.
1998–2001: Clinton–Lewinsky scandal and conflicts with online editors
Executive editor Joseph Lelyveld remained defiant against what he perceived as journalistic irresponsibility, leading The New York Times with alternate articles in the days following the death of Diana, Princess of Wales. In January 1998, Drudge Report published an article alleging Bill Clinton was involved in a sexual relationship with White House intern Monica Lewinsky and Newsweek had held off on publishing investigative reporter Michael Isikoff's article on the affair. Though The Washington Post and the Los Angeles Times published articles on the Drudge Report's articles, the Times did not. In The Washington Post, Frankel expressed contempt for organizations that chose to cover the story. The New York Times devoted little attention to Clinton denying the allegations on 60 Minutes. Lelyveld's hesitation subsided when special counsel Ken Starr, appointed in the wake of the Whitewater controversy, began formally investigating the scandal and sent several subpoenas. Then-investigative reporter Jeff Gerth was the first to report on a meeting Clinton had with his personal secretary Betty Currie in which discussed the investigation. The Clinton–Lewinsky scandal tested Lelyveld's commitment to journalistic standards and he reluctantly published a story from national editor Dean Baquet about a semen-stained dress Lewinsky had kept. The New York Times published its first issue in color on October 16, 1997.
On September 14, 1998, the hacker group Hackers for Girlies allegedly gained superuser access to The New York Timess servers and displayed pornographic imagery on the website in retaliation for Mitnick's arrest, in what constituted as the first cyberattack against a major news organization. Times employees were made aware of the intrusion at 10:20 a.m. but did not resolve the issue until 7:30 p.m. New York Times Electronic Media Company president Martin Nisenholtz suspected the cyberattack may have been timed to follow the release of the Starr Report several days earlier. The Times garnered controversy over its coverage of the federal government's investigation into Wen Ho Lee, a nuclear scientist employed at Los Alamos National Laboratory. Lee, unnamed, allegedly gave classified nuclear documents to China. Over the next eighteen months, The New York Times published over three hundred pieces in relation with the investigation into Lee and China's access to government secrets. In December 1999, Lee was indicted by a federal grand jury and imprisoned without bail. The punitive conditions of his confinement were criticized and The New York Times drew ire from civil rights groups for failing to investigate the Federal Bureau of Investigation's dubious claims. In September 2000, the Times ran an editors' note acknowledging its errors.
Editors in the newsroom often clashed with online editors. In July 1996, The Atlanta Journal-Constitution wrongfully identified security guard Richard Jewell as the suspect in the Centennial Olympic Park bombing during that year's Summer Olympics. Department of Justice reporter David Johnston cautioned against naming Jewell after Federal Bureau of Investigation senior officials told him they did not believe the case against Jewell was strong. While the print edition of The New York Times did not accuse Jewell, nytimes.com editors named him within a headline. The death of Diana, Princess of Wales represented a dictonomy between editorial editor Bernard Gwertzman and Lelyveld; her death warranted dynamic updates on the website. Gwertzman's faster pace reporting was antithetical to the beliefs of editors who did not want their names attached to incomplete or unpolished articles. Meislin and Gwertzman relied upon wire stories from Reuters and the Associated Press to ensure the website was frequently updated, motivating reporters who would balk at events they could have covered. In August 1999, managing editor Bill Keller called political editor Jerry Gray to propose he staff a twenty-four hour newsroom for nytimes.com. Like Keller, Nisenholtz was a critic of the traditional news cycle implemented on nytimes.com, believing that websites such as Yahoo and CNN were "kicking [The New York Timess] ass".
By 1999, the New York Times Electronic Media Company was operating nytimes.com, boston.com, nytoday.com, golfdigest.com, and winetoday.com. The company was also responsible for maintaining The New York Timess digital archives, including negotiating with news retrieval services such as Dow Jones & Company and LexisNexis. The prospects of making the Electronic Media Company a standalone company became more apparent as companies such as The Walt Disney Company and Barnes & Noble began spinning off their digital divisions. The servers hosting nytimes.com could not sustain increases in web traffic; the website crashed during the 71st Academy Awards and the Martha's Vineyard plane crash that killed John F. Kennedy Jr. In May 1999, Times Company Digital—later named New York Times Digital in March 2000—was made its own separate division that reported to The New York Times Company's corporate office, not the newspaper division. The New York Times Company announced a million () initial public offering of Times Company Digital with Goldman Sachs in January 2000. In October, the Nasdaq Composite crashed as part of the broader dot-com crash. New York Times Digital was forced to furlough over one hundred people and the company withdrew its initial public offering.
2001–2002: September 11 attacks