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Commuters crowd the escalators after getting off the subway at Yonge and Bloor on Jan. 2, 2019.Fred Lum

Toronto City Council agreed to continue contentious talks with the Ontario government on giving up ownership of the city’s subway system after hours of debate that laid bare how many unknowns remain.

The debate Wednesday also revealed the latest official cost projection for the Scarborough subway extension. Staff put this long-awaited figure at “just shy of $3.9-billion,” roughly double initial estimates from 2016 and more than the $3.56-billion in funding later approved by council.

Any concrete moves by the province to take over the subway remain some time off, and many issues remain to be ironed out. Among those that were highlighted Wednesday were the threat of derailing projects under way, the question of who pays for some of the changes the province has been seeking and the new approach the province wants to take on the downtown relief line.

Although numerous councillors and the mayor raised concerns about the prospect that the province would cause delays by changing existing transit plans – as Queen’s Park has pledged to do – most ultimately agreed that walking away from the negotiating table was too risky.

“That is the only way and the only place where we can stand up for Toronto and protect our transit system,” Mayor John Tory told reporters. “And I think it’s the only place as well where we can go to insist that the province show us, project by project, step by step, how the changes that are proposed do not result in delay.”

Speaking before Wednesday’s debate, Mr. Tory argued that “protests and demonstrations do not build transit,” leading critics to accuse him of failing to stand up for Toronto. For Councillor Josh Matlow, the mayor’s stand on the upload brought to mind the British Prime Minister’s flailing attempts to pursue a split with the European Union.

“I’m concerned that we have a mayor who hasn’t taken a clear position, even though council has,” Mr. Matlow said. “At this point I have more confidence in Theresa May leading the negotiations.”

Premier Doug Ford told the local cable channel CP24 that the province has a “better team” at Infrastructure Ontario and at the province’s transit agency, Metrolinx, that he said can build projects faster and more cheaply.

Neither of the agencies he cited has ever built a subway. Metrolinx, which is overseeing the construction, via a private consortium, of the Eglinton Crosstown light-rail line, runs GO Transit, a network of commuter-rail lines with a fraction of the ridership of the Toronto Transit Commission. One way the province hopes to save money on the relief line, according to a senior government official who was not authorized to speak publicly, is by building it as a “free-standing” line that would turn Pape station into an interchange like Bloor-Yonge station. The TTC, the official said, wants the new line built to allow trains to switch to it from the existing Bloor-Danforth line, requiring more tunnel infrastructure and a more complex renovation of Pape.

The cost of the Scarborough project emerged as well during Wednesday’s debate, about a week before it was expected to come to council. It came up because of fallout from a reference to the cost in letters sent to city staff this month by Michael Lindsay, the province’s special adviser on the upload. One of those letters stated that the Scarborough subway extension and downtown relief line had collectively doubled in price.

Staff pushed back on that notion Wednesday, saying that the latest Scarborough cost was roughly in line with the $3.56-billion figure approved by council, once related local improvements to public space and contingency funding were added in. It was not immediately clear exactly what was included or not included in their tally.

With a report from Jeff Gray