In the season premiere, flashbacks reveal how the president will officially announce his plans to run for re-election, which sends his staff into disarray as they work on the speech. But two problems dog them when Sam realizes that Bartlet never apologized for not disclosing his multiple sclerosis while C.J. makes a crucial gaffe during a press conference. Meanwhile, the chief executive has his own problems with wife Abbey who is still fuming that she was not consulted in his decision. Outside the Beltway, the president must decide if he should greenlight a military rescue of the besieged U.S. embassy in Haiti and chief counsel Babish informs Charlie to hire his own expensive lawyer before a special prosecutor begins looking into Bartlet's possible concealment of his illness.

From TV Guide:
"Yeah. And I'm gonna win." President Bartlet wastes no time in making his intentions clear as the third season begins (not surprisingly, that's the first question at the press conference that follows his MS disclosure). But everyone knows that his predicament will make the reelection campaign exceedingly difficult. Adding to Bartlet's problems is Abbey's reaction to his decision, not to mention Haiti's obstreperous dictator, who's giving national security adviser Nancy McNally fits. Meanwhile, the White House press corps is making life particularly miserable for C.J.

From NBC.com:
STORM CLOUDS GATHER OVER WHITE HOUSE IN PART I OF TWO-PART SEASON PREMIERE -- In the season premiere, flashbacks reveal how the President will officially announce his plans to run for re-election, which sends his staff into disarray as they work on the speech. But two problems dog them when Sam realizes that Bartlet never apologized for not disclosing his multiple sclerosis while C.J. makes a crucial gaffe during a press conference. Meanwhile, the President must decide if he should greenlight a military rescue of the besieged U.S. embassy in Haiti and chief counsel Babish (guest star Oliver Platt, "Bulworth") informs Charlie to hire his own expensive lawyer before a special prosecutor begins looking into Bartlet's possible concealment of his illness.