A different opening sequence shows Rhea Base prior to its destruction. The base's Russian crew are seen having trouble dealing with power surges before seeing an anomaly that is affecting Saturn's rings, which ultimately reveals to be the wormhole. The scene is expanded in the novelization.
A scene showing what happened to Thomas Whitmore after he fled his home at the beginning of the movie, which reveals he is at a bus stop and ranting his warnings about the aliens with two people. He is shortly found by Patricia and Agent Travis. He and Patricia then have the same dialogue from the bedroom scene though much longer. The scene appears in the film's novelization.
White House Destruction
In the original script the White House would have been destroyed (again) during the mothership's landing sequence. The scene would have shown the moment when the White House is almost destroyed by the mothership's landing strut, but only for a massive metal claw detaching from the strut and smashing into the White House. The scene was cut due to Roland Emmerich and his fellow editors not wanting to repeat the White House’s destruction from the original film.
Charlie Asks Rain Out
An extended scene of the roadside scene showing Julius consoling a distress Sam. Sam thanks Julius by telling him that he "would've made a really good grandpa." The scene appears in the film's novelization.
The scene shows President Lanford and Tanner being captured and imprisoned on the alien queen's ship after the aliens' attack on Cheyenne Mountain. The queen possessed Tanner to interrogate Lanford about the Sphere's location, thus explaining how the queen knew the Sphere was on Earth in the film. The scene appears in the film's novelization.
President Lanford's Death
A scene shows the alien queen alerted to the Sphere's location and saw no further use for Lanford, whom she crushed her to death.