The Kremlin's case against five Chechens accused of murdering liberal activist Boris Nemtsov for his "anti-Muslim" statements appears to be unraveling at lightning speed.

The alleged shooter, Zaur Dadayev, was likely tortured in custody and denied that he had confessed to the crime, a Russian human rights official said Tuesday after a prison visit.

Winston Churchill once said that following a Russian power struggle is like "watching two dogs fighting under a carpet," and Russians are now filling in the gaps in the official narrative of Mr. Nemtsov's death with a wave of speculation.

Most here believe that Mr. Nemtsov's assassination, a professional hit carried out under the Kremlin walls, is part of a deeper internecine battle. But there's little agreement or clarity on who is fighting who, and why.

Some experts see signs of blowback from Russia's covert war in Ukraine.

On Wednesday the opposition newspaper Novaya Gazeta published an unsigned analysis arguing that an extremist challenge to President Vladimir Putin's ruling circle could be underway. The paper suggests that ultra-nationalists, frustrated with Mr. Putin's failure to go all-out in support of eastern Ukrainian rebels and to silence fully his pro-Western domestic opponents, staged the killing of Nemtsov – in order to force the president to take responsibility for an act that to most Russians appeared to have official complicity.

"It's an unmistakable signal to the Kremlin that 'Russian patriots' are tired of waiting," the paper wrote. "[The message is that] If you don't do it somebody surely will. . . We are the force that protects your weakness and our task is to protect the Motherland from its enemies. . . Our work must be rewarded."

Free speech backlash

Last Sunday Russian investigators brought the five Chechen suspects to court, and charged two of them with carrying out the killing. The judge claimed that Mr. Dadayev had confessed to shooting Nemtsov, a former deputy prime minister.

Then the pro-Putin leader of Chechnya, Ramzan Kadyrov, took to his Instagram account to claim that Dadayev, who had served as an officer in Chechnya's security forces, was a devout Muslim who'd been shocked by the Charlie Hebdo cartoons and may have killed Nemtsov over his outspoken defense of free speech.

"All who know [Dadayev] confirm that he is a deep believer and also that he, like all Muslims, was shocked by the activities of Charlie and comments in support of printing the cartoons," Mr. Kadyrov wrote. "If the court confirms Dadayev’s guilt, then he’s committed a serious crime... But I want to point out that Dadayev was incapable of lifting so much as a finger against Russia, a country for which he spent many years risking his life."

That framed Nemtsov's killing in a way that let both the Kremlin and Kadyrov off the hook. The very next day Putin awarded Kadyrov with the Order of Honor, which recognizes exemplary public service.

Some speculate that Kadyrov, who has sent large numbers of Chechen fighters to aid east Ukrainian rebels, was behind Nemtsov's murder. Others suggest that Chechens opposed to Kadyrov, or even Russian security officials, may have done it to drive a wedge between the Chechen strongman and the Kremlin.

Kremlin loyalist

Kadyrov was left in near total charge of Chechnya after Russian forces pulled out in 2009 after pacifying the rebellious republic. He professes total loyalty to the Kremlin, yet has infuriated many by running Chechnya as his fiefdom, largely outside of Russian law.

"Chechnya is an enclave where power has been monopolized [by Kadyrov] to such an extent that the place can be described only with great reserve as part of Russia," says Gennady Gudkov, a former KGB officer and parliamentarian turned anti-Kremlin activist.

The theory advanced by Kadyrov is falling apart. Dadayev insisted Tuesday that he had not made a confession during a visit by Andrei Babushkin, a member of the Kremlin's human rights commission. Mr. Babushkin later told journalists that there were signs Dadayev had been tortured.

Meanwhile, Nemtsov's friends excavated his Facebook postings at the time of the Charlie Hebdo massacre and found that, aside from some generic affirmations of free speech, the liberal activist hadn't said anything that would likely rile Muslims.

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Chechens have often been blamed for political killings in Russia, without the actual organizers ever being named or brought to justice. Notably, five Chechens were convicted in the 2006 slaying of investigative journalist Anna Politkovskaya; the crime's "mastermind" and his motives remain unknown.

"Chechens are used as killers, but also as smokescreens," says Andrei Soldatov, editor of the online security journal Agentura.ru. "Kadyrov protects his people, and that's why investigations of these murders stop at the immediate perpetrators and never go up the chain.