Even if Mr. Junqueras had been released, his claim to take charge of Catalonia would have come up against that of the region’s former leader, Carles Puigdemont, whose remodeled party unexpectedly won the most seats among the separatist groupings in the Dec. 21 vote.
Mr. Puigdemont is now asserting his right to re-election from Belgium, without specifying whether he plans to return to Catalonia.
He surfaced in Brussels in late October, alongside some other members of his former cabinet, shortly after Mr. Rajoy had responded to the independence declaration by ousting them from office and taking charge of Catalonia.
Mr. Rajoy then called a snap regional election, hoping Catalan voters would decisively reject secessionism. Instead, the three main separatist parties won 70 of the Catalan Parliament’s 135 seats, on 47.5 percent of the vote — almost exactly the share they achieved in the previous election in 2015.
While the separatists narrowly kept their parliamentary majority, their numbers might not add up, because eight of their 70 elected lawmakers are either in jail in Madrid or in Belgium alongside Mr. Puigdemont, refusing to return to Spain and risk prosecution.
Mr. Puigdemont is demanding guarantees from the Spanish authorities that he can resume his role as the “legitimate” leader of Catalonia. After the Dec. 21 election, he asked to meet Mr. Rajoy for negotiations outside Spain, a proposal Mr. Rajoy rejected.
He later described as “absurd” the idea that Mr. Puigdemont could somehow lead Catalonia from Belgium.
When separatist parties found themselves in a postelection deadlock two years ago, Mr. Puigdemont, a former city mayor, emerged as a compromise candidate. Now, however, his legal problems, coupled with his electoral success, have thrust him into a very different role, one in which he may prove an obstacle to the formation of a new government.
“The great paradox is that Puigdemont turned out last month to be a surprising electoral asset, who managed to lead his party almost single-handedly from Belgium, but his claims now make everything more complicated,” said Mr. Simón.
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The Catalan Parliament will reconvene on Jan. 17, according to Mr. Rajoy’s schedule, and then vote on a new government. It’s uncertain who will be seated in the hemicycle, and whether the ineligible separatists will try to pass their seats to substitute candidates.
Even if the separatists can overcome this major hurdle, they may struggle to find a path forward after four months of political turmoil that included an unconstitutional referendum and a botched attempt to declare independence.
The smallest of the separatist parties — the far-left Popular Unity Candidacy — is adamant that Catalonia can break away from Spain unilaterally, which could divide it from other parties that have been more cagey about their plans.
“What happens next for the independence movement depends on several unknowns, but perhaps mostly on Puigdemont, a leader whose main trait has become his complete unpredictability,” said Josep Ramoneda, a political columnist.
After the flight to Belgium, Mr. Ramoneda said, Mr. Puigdemont “can talk as much as he wants about his legitimacy, but he’s also trying to get out of a very difficult personal situation.” He described Mr. Puigdemont’s efforts to force Mr. Rajoy into a negotiated settlement as “pure fantasy.”
The Catalan election may in fact have left Mr. Rajoy with less freedom to maneuver, because his Popular Party came last. Instead, the biggest single vote-getter was another unionist party, Ciudadanos, on whose support in Madrid Mr. Rajoy’s own minority government depends.
Unless the separatists succumb to their internal tensions and legal problems, that victory will only make Ciudadanos the main opposition in Catalonia. But it does give the party an opportunity to raise the pressure on Mr. Rajoy, and strengthens its claim to take charge in the conflict as the flag bearer for Spanish sovereignty.
“The only thing that now keeps Rajoy in office is not his own strength but the weakness of those who oppose him,” said Mr. Ramoneda.
While the politicians squabble, Spanish judges are showing no sign of softening their stance toward the Catalan separatists, even if that could help break the political deadlock.
Spanish legal experts have defended the prosecution of the separatists for civil disobedience, but have disagreed over whether the charges could include rebellion, which carries a maximum prison sentence of 30 years.
Writing this week in the newspaper El País, José María Ruiz Soroa, a lawyer, argued that the stalemate in Catalonia had allowed the judiciary to take center stage and undertake “a radical mutation of the rules of the Spanish constitutional game,” by criminalizing the independence drive.
During his appeal, according to his lawyers, Mr. Junqueras told the judges of the Supreme Court that he was a “man of peace,” who espoused Christian values and dialogue. But on Friday, the judges voted unanimously to keep him in jail.
His conduct as deputy leader of Catalonia, the judges’ ruling said, had shown that Mr. Junqueras wanted to force Catalonia’s independence and was willing to endorse “predictable and highly probable
episodes of violence to reach the proposed goal.”