The President was President of the United States during the events of X-Men: The Last Stand.
Prior to the events of The Last Stand, the president was elected on a platform that was more conciliatory towards mutants. Replacing President McKenna, the new president, acting on the promises of his platform, created a new executive department and cabinet position to deal with mutant issues - the Department of Mutant Affairs. Dr. Hank McCoy, a long-time mutant rights advocate, was appointed as the department's first Secretary.
Despite such conciliatory moves towards mutants, however, the president still had to deal with the omnipresent threat posed by Magneto and the Brotherhood of Mutants. He was often in the Situation Room conferring with his Secretary of Defense Trask and various military officials as to how to deal with the Brotherhood and other mutant terrorist groups.
The President's administration, in partnership with Worthington Labs, developed the mutant cure. Publicly, Worthington Labs promoted the cure as a voluntary way of dealing with mutation. Privately, the cure was already being integrated into weapons - initially to federal security forces - as a contingency plan to deal with threatening mutants. Following the Brotherhood's attack on the prison convoy carrying Mystique, they discovered and made public the fact that Worthington's cure was being weaponized. Upset that mutant policy was being made without his input, McCoy resigned his cabinet position.
As the Brotherhood began to carry out attacks on locations administering the cure to volunteering mutants, the President authorized that the cure be further weaponized, resulting in U.S. National Guard troops being re-equipped with plastic weapons (as a counter-measure against Magneto specifically) loaded with cure cartridges.
Following the incident on Alcatraz, the President appointed Hank McCoy as America's U.N. Ambassador, ostensibly for his service in combating the Brotherhood's threat.