The transit strike may have ended, but the war over government pensions has just begun.

The quick end to the bitter transit strike that was barely in its 60th hour came without a contract agreement that would resolve the financial crisis over rising pension costs that plague the Metropolitan Transportation Authority.

The strike’s contentious days disclosed the depths of the feelings on both sides of the pension issue. The MTA’s effort to change the pensions of its employees brought the issue to the public’s attention.

If changes spread beyond the MTA, it could mean billions in savings for taxpayers. Workers may benefit from the changes, too, some advocates have argued, if they can take their retirement funds with them to another job or will them to their heirs. But the union does not see it that way, setting the stage for a struggle that some say will persist long past the strike’s end.

“This is not the end of it, this is just the beginning,” the director of the Manhattan Institute’s Empire Center for New York State Policy, E.J. McMahon, said. “I think the public has now been forcefully confronted by the issue. What Toussaint has done is educate a whole new generation of New Yorkers as to how cushy pension deals are for workers by private sector standards.”

Mayor Bloomberg, who softened his tone after the strike was called off yesterday, said rising pension and medical costs were a “serious issue for every municipality.” The government can no longer afford to maintain the current pension system for future government employees, Mr. Bloomberg said.

“Things do come home to roost,” Mr. Bloomberg said. “You cannot go on and have good things today and postpone the cost for the future.”

The director of the National Center for the Study of Collective Bargaining in Higher Education and the Professions at Hunter College, Richard Boris, said the MTA miscalculated by thinking it could address pensions at the negotiating table with one union without dragging the rest of the unions into the fray.

“The unions are saying if you change the model, you have to have a conversation at the table with all of us,” Mr. Boris said.

Mediators, who spent 12 hours straight beginning at 1 a.m. yesterday shuttling between hotel rooms in an effort to broker a truce between the authority and the Transport Workers Union Local 100, revealed little of the possible details of a new contract, insisting on a “media blackout” to help calm the nerves and emotions of the two sides as they hammer out a contract.

But it appears unlikely that the MTA will win a major concession from the union that would help it significantly address its pensions concerns. The authority had already relinquished its demand that new employees retire with a full pension at the age of 62 instead of 55, as current employees do.

The lead mediator, the director of conciliation for the state’s Public Employment Relations Board, Richard Curreri, hinted yesterday at a possible exit strategy that would allow the authority to begin addressing its soaring health care costs and pension liabilities, which total $2.2 billion.

Mr. Curreri, who said he had not slept for 30 hours, said the mediators could not ask the MTA to take the pension issue off the table “without assurance that the TWU is willing to review alternate means to address those challenges, such as the rising cost of health benefits.”

The statement suggested that the union may agree to pay more toward their health benefits, either a percentage of their wages or a higher co-pay. The authority last asked the workers to pay 1% of their wages toward health benefits.

Workers returned to the subways and buses yesterday without a contract after the union’s executive board voted overwhelmingly to end the strike, despite the objections of five members who had sought a guarantee that workers would not lose two days’ pay for every day off the job.

One executive board member, George Perlstein, who voted against returning to work, said it defeated the purpose of the strike, which was to use the paralysis of a citywide transit shutdown to wrest a contract to the union’s liking.

He said, standing outside the union’s headquarters shortly after the vote, that surrendering the union’s biggest bargaining chip – a strike – and returning to work without a contract was “unconscionable,” especially since the union president, Roger Toussaint could not guarantee his members amnesty from the Taylor law fines.

“I got here an hour late because I could not hang up the telephone,” he said. “People were screaming bloody murder: ‘full amnesty, full amnesty, full amnesty.’ We got nothing. Absolutely nothing.”

Half an hour later, Mr. Toussaint emerged from the union’s headquarters on the West Side of Manhattan, a smile of relief on his face.

“We thank our riders for their patience and forbearance,” Mr. Toussaint said in a statement that was uncharacteristically short.

While the decision to pursue the fines rests with the MTA, a Supreme Court judge, Theodore Jones, in Brooklyn held off on deciding whether to jail the union president and his top two deputies for violating a restraining order the court issued last week barring a strike.

After union lawyers were unable to make the 4 p.m. hearing because they were stuck in traffic, Judge Jones postponed the hearing until January 20, saying he did not want his decision to be used as a chip at the negotiating table.

“I want the negotiations to take place in an atmosphere in which the court is not perceived to be influential to either side,” Judge Jones said.

It has been the mediators – Mr. Curreri and two others, Martin Scheinman and Alan Viani – who so far have had the greatest influence on discussions. They managed to get the two parties to return to the negotiating table and the workers to return to the rails.

“You get them focused on the issues and get them unfocused on the strike itself because that is what’s fueling the emotions,” Mr. Curreri said. “To the parties’ credit, it didn’t take them very long to get past that.”