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When teachers at Thomas Gardner Elementary School voted in fall 2003 to join Boston鈥檚 network of 鈥減ilot鈥� schools, they had no inkling of the political firestorm that lay ahead.

But a few months after they moved to become part of the city鈥檚 nationally watched experiment with small, autonomous public schools, the president of the Boston Teachers Union put the kibosh on the plan. Now, whether the 300-student school will ever make the switch hangs on the outcome of an increasingly bitter standoff between the Boston school district and the 7,000-member BTU.

鈥淭his is far more than the teachers bargained for,鈥� said David F. Simon, a local philanthropist who has strongly backed the school鈥檚 push for pilot status. 鈥淭hey never imagined in their wildest dreams that they would get caught in the middle of this.鈥�

A major sticking point is whether teachers at all the city鈥檚 17 pilot schools should be paid overtime for hours they work beyond those specified in the districtwide contract. How the dispute gets resolved, some observers say, may resonate well beyond the borders of the 59,000-student district.

鈥淲hile the pilot school controversy is a particular controversy in a particular place, I think that it speaks volumes about this larger issue, which is how are schools going to be organized and run in the future,鈥� said Paul S. Grogan, the president of the Boston Foundation, a local philanthropy that supports pilot schools.

Often billed as the district鈥檚 answer to charter schools, Boston鈥檚 pilot schools are the fruit of a deal reached 11 years ago between the district and the BTU, the city鈥檚 affiliate of the American Federation of Teachers, and enshrined since then in a succession of labor contracts.

The schools are exempt from union work rules鈥攁lthough they follow the standard pay scale鈥攁nd get autonomy over their budgets, curricula, and hiring.

But since he ascended to the union鈥檚 top spot two years ago, BTU President Richard F. Stutman has pressed to curb what he sees as abuses of the schools鈥� authority.

Some of the schools require teachers to put in longer days and to devote some summer days to planning and training, for example. Individual schools decide whether to give stipends for that work鈥攕ome do and some don鈥檛鈥攁nd Mr. Stutman says that is unfair.

鈥淚t鈥檚 the principle,鈥� Mr. Stutman said in a recent interview. 鈥淚t鈥檚 forced overtime. [Teachers] cannot stay in the school without working that extra time.鈥�

Money at Issue

The district and its allies argue that pilot teachers know what they鈥檙e getting into and have the right to transfer to other schools if they want out. And they say forbidding schools to set calendars that depart from the contract would erode the flexibility that has helped make pilot schools a popular option in a district that continues to lose enrollment to charter schools.

Besides, the district doesn鈥檛 have the money for a uniform overtime policy for pilot schools, officials argue.

鈥淲e鈥檙e not interested in a solution that requires the city to spend more money,鈥� said Michael Contompasis, the district鈥檚 chief operating officer. 鈥淎nd we鈥檙e not interested in limiting the flexibility that the existing pilots already have.鈥�

Conceived on the heels of Massachusetts鈥� 1993 law authorizing charter schools, pilot schools were seen as introducing new choices into the public system while serving as models of innovation.

In contrast to the city鈥檚 18 charter schools, the pilot schools are considered part of the Boston school system and their teachers belong to the local union. After the first five pilot schools opened in 1995, growth was gradual until a flurry of start-ups and conversions swelled their ranks from nine schools in the 2001-02 school year to 17 schools by fall 2003.

In June of that year, the presidency of the BTU changed hands for the first time in 28 years. Mr. Stutman came to office promising to guard teachers鈥� wages and benefits at a time of budget cuts and shrinking enrollment.

As he bargained for a new contract, the union chief presented a list of demands for policy changes in pilot schools. The two sides opted last year to table their disagreements in the interest of signing their overdue three-year pact, which they did in the spring of 2004.

Unfortunately for Gardner Elementary School, its teachers voted to 鈥済o pilot鈥� in the fall of 2003, as the union was staging a work slowdown amid contract talks. Conversions to pilot status need approval from a district-union steering committee鈥攅ither the district superintendent or the union president can veto the plans鈥攁nd that committee didn鈥檛 meet during the contract dispute.

When Gardner鈥檚 proposal finally came before the committee in June of last year, Mr. Stutman decided to make a stand to push the district to address his broader demands. 鈥淲e have no other leverage,鈥� he said in the interview.

Now, with the two sides still unable to agree a year later, the district and other pilot school supporters are looking for leverage of their own. A bill in the Massachusetts legislature would raise a cap that is limiting the growth of charter schools in the city. To date, both the district and the union have strongly opposed that measure.

But some pilot school supporters, including the Boston Foundation鈥檚 Mr. Grogan, have urged the city to reconsider as a means of getting the union to budge. In late April, Boston Mayor Thomas M. Menino, a Democrat who appoints the city鈥檚 school board, publicly suggested that he was so frustrated with the union that he just might do that.

Meanwhile, other city politicans have been pressuring Mr. Stutman, in part because of complaints about Gardner Elementary鈥檚 status and the pall it has cast over plans for more pilot schools. Among them is state Rep. Michael J. Moran, a Democrat who says he strongly supports organized labor, opposes charter schooling, and champions public education.

鈥淭he pilot schools provide the school system with the type of reforms that it needs to attract more children into the public school system,鈥� said Mr. Moran, whose district includes Gardner Elementary. 鈥淚 want the situation to be worked out.鈥�