2016–2017: Dhoni biopic, Raabta and Kedarnath
In 2011, a biopic on the life of the Indian cricket team captain Mahendra Singh Dhoni was conceived by Dhoni's manager, Arun Pandey. The project was initially faced with various difficulties including objections from the Board of Control for Cricket in India (BCCI) and Dhoni's demand for a large royalty. On 25 September 2014, Sushant Singh Rajput was announced as the actor who would play the role of Dhoni in the biopic which was titled M.S. Dhoni: The Untold Story and directed by Neeraj Pandey. The film was centered around the life of the cricketer beginning with his childhood in the city of Ranchi and leading up to the 2011 Cricket World Cup victory for India under his captaincy. Incidentally, Rajput wasn't adept at cricket and had to train regularly in the game for 13 months as well as capture the playing style of Dhoni for his portrayal in the film, he was coached by Kiran More who reportedly trained him in the regimen of a professional sportsperson rather than as an actor. The film was produced by Arun Pandey with Fox Star Studios and released on 2 October 2016. It became the 5th highest grossing Bollywood film of that year. Rajput received critical acclaim for his performance and nominations to a number of awards, including the Filmfare Awards, the International Indian Film Academy Awards and the winning nomination at the Indian Film Festival of Melbourne. He also made a cameo appearance in the comedy film Welcome to New York, which was released on 23 February 2018 and where the lead characters met Rajput but confused him for Mahendra Singh Dhoni.
During the release of M. S. Dhoni: The Untold Story, Rajput in an interview had stated that he was signed up to do five more films; namely Raabta, Takadum, Chanda Mama Door Ke, another biopic of an athlete and a film produced by Dharma Productions featuring Jacqueline Fernandez. Earlier in 2014, reports had emerged that Rajput was being signed in alongside Alia Bhatt for the starring roles in the largest budget production of the producer–directors Homi Adajania and Dinesh Vijan. In an announcement in February 2015, the film titled Raabta, produced by the Vijan owned Maddock Films and co-directed by Adajania and Vijan was publicised where Rajput and Bhatt were in the lead role. Bhatt however decided to opt out of the project in the same year, and the role of the female lead eventually went to Kriti Sanon. Rajput and Sanon later featured in a 2017 T-Series music video of the song named Paas Aao, composed by the duo Armaan and Amaal Mallik. In 2017, he was featured for first time in the Forbes India's Top 100 Celebrity list.
The second biopic that Rajput was to feature in was tentatively titled as Murli: The Unsung Hero, where he would play the role of the disabled jawan turned Paralympics gold medalist Murlikant Petkar. In June 2016, Rajput along with Parineeti Chopra and Irrfan Khan were also announced as the lead of the Adajania directed film called Takadum with shooting scheduled to begin in October but the project was being put on hold due to issues related to script re-adaptation. Meanwhile, the announcement of Rajput's role in Chanda Mama Door Ke had come in September 2016. In the film which was to be directed by Sanjay Puran Singh, Rajput would have starred alongside R. Madhavan and Nawazuddin Siddiqui and was cast in the role of an astronaut, for which he was even sent to NASA on a training module in 2017. He was also cast as the lead in the spy thriller film Romeo Akbar Walter in 2017, however he quit the project in the same year reportedly causing displeasure to the producer Bunty Walia who had publicised the film with him on the cover. Later in December 2017, it was announced that he was signed in by Abhishek Chaubey, the director of Udta Punjab for his next film titled Sonchiriya, where he would star alongside Bhumi Pednekar.
Raabta was released on 9 June 2017, which subsequently received mixed reviews from critics and emerged as a flop in the box office, unable to recover its large production cost. It was a time transcending love story, where Sushant Singh Rajput played the role of two characters who were reincarnations of each other. While the filming was primarily carried out in the city of Budapest, Hungary, in the Indian state of Punjab and in the island country of Mauritius. Earlier in March 2017, Rajput had also begun shooting alongside Jacqueline Fernandez for Karan Johar's Dharma Productions film, by then titled as Drive. The film was directed by Tarun Mansukhani and was a prequel to the 2014 film Bang Bang!, that had featured Hrithik Roshan and Katrina Kaif. Part of the shooting occurred in the city of Tel Aviv, Israel which was promoted by the Government of Israel as a part of its tourism and diplomatic initiative. The release was initially scheduled for 2 March 2018, but in a February announcement, the date was moved to 7 September 2018. The release was however postponed for a second time with no fixed release date due to creative disagreements between the director Mansukhani and the producer Karan Johar.
In the meantime in March 2017, Rajput was signed in by the director Abhishek Kapoor and the producer Ekta Kapoor for their film called Kedarnath. It was a love story set in the backdrop of the 2013 floods in Uttarakhand, where Rajput co-starred with Sara Ali Khan. He played the character of Mansoor, a Muslim porter who was also a devotee of Lord Shiva and whose livelihood revolved around the Shiv temple at Kedarnath. The shooting of the film began in September 2017 and was set to release by June 2018. During the shooting, Abhishek Kapoor who had previously been the director of Rajput's debut film Kai Po Che!, stated that Rajput was in much better form for Kedarnath and expected it to become an even bigger success. The film however soon became embroidered in controversy as the Bharatiya Janata Party alleged that it was promoting Jihad by showing an interfaith couple and called for the imposition of a ban on it. In the end, the film was banned from screening in 7 out of 13 districts in Uttarakhand and released on 7 December 2018. Despite the ban, it became a commercial success, although it didn't completely meet the projected success in the box office. Following the release, it was the second highest grossing among Rajput's starring films after the Dhoni biopic.