They say Lankesh's killers were associated with Sanatan Sanstha, a shadowy extremist religious sect that has been accused of using hypnotherapy to incite its followers to kill those they consider enemies of Hinduism. Investigators uncovered a hit list of more than two dozen other writers and scholars.
The hit list and the accusations against members of Sanatan Sanstha have frightened intellectuals and raised concerns about freedom of expression in the world's largest democracy at a time when violence by fringe Hindu extremist groups - many of whom helped propel India's governing Hindu nationalist Bharatiya Janata Party to power - appears to be rising.
"There is no doubt about it. This is an organised group of individuals who planned and executed all four murders, and some of those who are arrested are followers of Sanatan Sanstha," said B.K. Singh, the head of special police team investigating Lankesh's murder.
On August 27, at a news conference in Mumbai, members of the sect - clad in the colour saffron, sacred to Hinduism - denied the accused were part of their organisation.
"They must have attended our meetings and must have been staunch supporters of [the Hindu cause], but that does not mean they have been a part of Sanatan Sanstha," said Chetan Rajhans, the group's spokesman.
Now Indians wonder who is next.
The shooting deaths of the three other secular intellectuals in recent years bear striking similarities to Lankesh's killing, investigators say.
In 2013, gun-toting assailants on motorcycles killed doctor and activist Narendra Dabholkar; two years later, others shot and killed Communist Party leader Govind Pansare, who was also out for his morning walk. The same year, writer M.M. Kalburgi was shot and killed at point-blank range when he answered the door of his home.
Police contend that Sanatan Sanstha is the common thread: The accused gunman in the Pansare murder was a member of Sanatan Sanstha. Forensic tests show the gun used to kill Kalburgi was also used in Lankesh's murder, and an associate of Sanatan Sanstha is among those held in judicial custody in Lankesh's death. None of the suspects in these cases have been convicted.
The suspects in Lankesh's killing used code names, but they also kept detailed diaries, which have been a boon to investigators in the wide-ranging investigation into the alleged extremist cell. One suspect kept a notebook that contained a map of Lankesh's neighbourhood. Another kept a hit list.
An alleged recruiter for the group who was also arrested told police the suspects often took months to plan an attack, casing their targets' homes and memorising daily routines, his statement shows. They recruited religious young zealots as triggermen, then sent them to arms training on a remote farm, investigators say.
The alleged ringleader of the extremist cell, Amol Kale, a 37-year-old machine shop owner from Pune, was arrested in May in connection with Lankesh's murder. Investigators say he provided arms and training to assailants in other attacks and that he has been associated with Sanatan Sanstha for over a decade.
Kale kept a coded diary with the names of targets and a chilling "to do" list for future killings, including details such as who would bail the assailants out of jail if they were caught, investigators said. Kale's lawyer said his client is innocent and confessed because he was beaten in custody, a charge police deny.
Parashuram Waghmare, an unemployed 26-year-old who investigators say appeared in the closed-circuit footage of the killing, told police he scarcely knew who Lankesh was when he shot her. "I killed her for my religion," he said, according to an investigator of Lankesh's murder. Police believe Kale hired Waghmare to carry out the killing.
Allegations of violence have dogged Sanatan Sanstha since long before the deaths of the intellectuals. Members of the group were convicted in two small bomb blasts in 2008, and two followers accidentally blew themselves up trying to plant a bomb at a crowded religious festival in 2009. State authorities pressed the Indian Government to ban the group as early as 2011.
Violent rhetoric can be traced back to the group's founder, Jayant Athavale, a London-trained doctor who became convinced he was an incarnation of the Hindu god Vishnu with a mission to establish a "Hindu nation" in India, according to his website. About 500 followers spend their days chanting mantras, doing chores and editing the group's newsletters in a spiritual retreat in India's coastal haven of Goa, according to Rajhans, the sect's spokesman.
Athavale, now 76 and rarely seen, has advocated violence as part of a "religious war," according to one of his early books, The Duties of a Warrior.
"It is very important that we slice/kill the evil-minded from the society," Athavale wrote. "Ours is a land of saints, we would not allow anarchy to perpetuate."
Police say Athavale once hoped to amass a huge army for his cause but eventually the focus shifted to targeting prominent secular scholars he believes are "durjan" - enemies of Hinduism.
Critics charge these fringe groups are gaining strength in the current political climate in India, where Narendra Modi's Hindu nationalist government has been criticised for doing little to stop religious violence.
The sect has long maintained it is a spiritual organisation.
"Sanatan Sanstha has no connection with these killings," Rajhans said in an emailed response to questions. "All these allegations are baseless."
Relatives of followers who have filed a lawsuit in Mumbai allege Athavale used manipulative hypnosis techniques to separate them from their families, coerce them into giving their money and incite them to violence, court records show. They have submitted The Duties of a Warrior as evidence in court.
Rajhans also refuted that allegation: "Nobody can be hypnotised against his wish and cannot be made to commit any evil deed. Therefore, such false things are spread only to defame Sanatan Sanstha."
Lankesh had been an iconoclast her whole life, rejecting the constraints of India's traditional society even as a young girl, her sister Kavitha, 53, a filmmaker, recalled in an interview.
When her family tried to marry her off to a doctor, she went to the beauty parlour and got her hair cut short as a boy's, she recalled.
"It was like a Bollywood movie," Kavitha Lankesh said. "The guy wanted to marry her anyway!"
She championed the rights of women, India's lower caste and indigenous peoples, and wrote columns taking on establishment politicians and religious zealots - whom she dubbed "the lunatic brigade" - without fear.
Toward the end of her life, Lankesh, 55, was increasingly worn down by the demands of trying to keep her tiny newsweekly afloat while fighting defamation cases and online trolling, friends said.
Lankesh's death came as journalists and secular activists in India are being intimidated, jailed and killed for their work.
"People are more circumspect now about what they write and what they say. Your words can be misinterpreted and twisted very consciously," said Umar Khalid, 31, a well-known student activist and friend of Lankesh.
