The USS Enterprise NCC-1701, is accidentally sent back in time to Earth to the 1960's by the effects of a "black star". Enterprise appears in Earth's upper atmosphere and is detected by military radar.
Labeled a UFO, a U.S. Air Force F-104 interceptor, piloted by Captain John Christopher, is scrambled to identify the craft. Fearing an attack, Captain Kirk orders a tractor beam to be used on the jet, which causes it to break apart. To save the life of the pilot, Kirk orders they beam him aboard the Enterprise.
The rest, as they say, is history...