Early in the Clinton administration, terrorists struck in the United States. A car bomb left in an underground parking garage exploded in the heart of New York City's financial district in February of 1993. The World Trade Center bombing killed six people, injured more than 1,000 others, and caused around $600 million worth of damage. The next year, four members of a militant Islamic group were convicted in connection with this incident. In another New York case, ten Muslim militants were convicted of conspiring that same year to bomb the United Nations headquarters, two tunnels, and other prominent New York landmarks. Their convictions were handed down in 1995.

Also in 1993, members of a heavily armed religious sect calling themselves the Branch Davidians held a fifty-one-day standoff with law-enforcement officials near Waco, Texas. When negotiations failed, federal agents stormed the complex, resulting in the death of eighty Branch Davidians and four agents. Attorney General Janet Reno accepted responsibility for giving the go-ahead.

On April 19, 1995, terrorism struck in America's heartland. A blast caused by a huge car bomb blew open one whole side of the Alfred P. Murrah Federal Building in Oklahoma City, killing more than 168 people, at least 15 of whom were children in day care. It was the worst act of terrorism on U.S. soil at that time. Understandably, it outraged a nation, especially because the act had been committed by an American. The FBI arrested their key suspect, twenty-seven-year-old Timothy McVeigh, who harbored a far-right political agenda and alliances to paramilitary groups. Terry Nichols was also charged in the crime. Believers in this extremist group encouraged others to stockpile weapons, because they feared the government was plotting to take away their rights.

During the 1996 Summer Olympics held in Atlanta, Georgia, a pipe bomb exploded in an outdoor park. Also in 1996, the FBI finally caught up to a mail bomber, Ted Kaczynski, in the back woods of Montana. Authorities had been chasing after the “Unabomber” for twenty years.

Though Clinton had to work with a Republican Congress, he was able to pass legislation to help combat terrorism, making it easier to deport foreigners suspected of terrorist activities.