NOTWITHSTANDING the faith that miillions of Filipinoes had reposed in the elections, the thought that they might deliver the Philippines to a smooth new beginning did not survive the polling on Friday. Not only Mrs. Aquino, but also foreign observers without an ax to grind, including Sen. Richard Lugar, at once faulted the way President Marcos had run the process. And yesterday, as even the official early count showed Mrs. Aquino in the lead, Mr. Marcos warned he might void the vote rather than concede defeat.

It is a volatile situation and President Marcos, his power challenged, should not be underestimated. But surely most Filipinoes, including many who voted for him, can see the country's vital interest in allowing the outcome of the election to reflect the popular will. This means first of all continuing the counting and permitting the independent vote- checking that alone can give the opposition confidence in the results -- and indeed in the political process as a whole.

Confidence was always the real issue in the elections. The United States so recognized by emphasizing throughout that the purpose of the exercise was to create a mandate the people found credible. Without such confidence, the Philippines, already facing a corrosive economic crisis and a rampant communist insurgency, may find itself moving toward civil war.

If it comes, let it be plainly understood how. President Marcos broke the rather forgiving rules of Philippine politics by ruling too long, too harshly, too arbirtrarily and too greedily. Still, the democratic process offered his country a way to return to the habits of a more civil and orderly society. If Mr. Marcos cannot exercise the restraint necessary to assure his troubled country fair use of that process, he will bear the responsibility.

Some of the remarks he made yesterday in the course of threatening to stay in power had a barbed edge. Mr. Marcos seemed to be saying that American concern over the fairness of the elections amounts to American "abandonment" of its longtime ally. Actually, he is the one who by his conduct is shredding this traditional tie. He also wanted it known -- another veiled threat -- that the American bases at Clark and Subic Bay were in the balance, suggesting that if the Americans left he would be impelled to find a way to accommodate "the other powers in the region."

He is right: the bases are important to the United States. But they are not more importanmt than the condition of democracy in the Philippines. And most Americans understand it is foolish to think of retaining access to the bases in circumstances of official threat or spreading unrest. It is not the United States but the Phillippines which is teetering on the brink of calamity.