Prior to the start of filming, Keanu Reeves had injured himself playing a pickup game of hockey in his native Canada. He injured his neck and back areas causing him to gain weight which explains his look in the film.
The massive explosion seen early in the film caused by the botched cold fusion project was shot with miniatures with an old abandoned steel factory acting as both the interior and exterior for the shots.
The drawbridge sequence where Keanu Reeves is being chased by the Chicago P.D., F.B.I. and Brian Cox's henchmen took approximately one week of night shoots to film with temperatures ranging from five below to twenty below zero.
Scenes filmed at both the Field Museum of Natural History and the Museum of Science and Industry, both in Chicago (about five miles apart), were combined to suggest a (fictitious) museum located outside of Washington, DC. The action did not occur in Chicago.
The motorcycle in the movie is a 1976 Kawasaki KZ1000, requested by Keanu Reeves himself. Fox bought five bikes for different scenes, all painted flat black to prevent the spotlights from being reflected.
The scene in which Keanu Reeves barely escapes on the motorcycle was shot mainly with blue screens and explosion effects added in post-production. The live sequences had Reeves riding a motorcycle hooked up to the back of truck with a camera filming tight close ups.
The ramp Keanu Reeves runs down during the explosion is located at Argonne National Laboratory in Argonne, Illinois. The ramp is located at the IPNS (Intense Pulsed Neutron Source) facility and can be seen in aerial photos on the division's website.
Elements of the original script of the film written by Josh Friedman entitled "Dead Drop" in which Morgan Freeman's character in the film frames Keanu Reeves' character for murder and industrial espionage were kept with subsequent rewrites, with the final shooting draft of the script having Freeman playing more of a mysterious mentor-like government agent and Reeves' character still a scientist plus adding the Rachel Weisz character.
There is a sequence in the movie that is supposed to take place in the U.S. Capitol Building in Washington, D.C. The exterior of the D.C. landmark is shown, but the Wisconsin State Capitol, located in Madison, Wisconsin, was used for the interior shots. Two scenes were filmed there: one in the first floor of the Wisconsin Capitol rotunda, and one in the building's Supreme Court chamber.
'Paul Shannon' smokes Davidoff cigars throughout the movie. It's not possible to tell whether they are the Dominican-made or Cuban-made brand because the bands are identical. Morgan Freeman takes a cigar out of his cigar case during the FBI interview in his home (at around 55 mins). It is a Savinelli 3-finger Churchill-length case in brown leather.