[7] During the 2012 Badakhshan Mountainous Autonomous Region clashes, government military forces entered Khorugh, intending to assassinate both Tolibbek Ayyombekov and Muhammadboqir Muhammadboqirov in order to take full political and economic control of the area.

Although Ayyombekov surrendered and former opposition commander Imomnazar Imomnazarov was killed, Muhammadboqirov was able to survive the events, remaining one of the last few independent political leaders in the autonomous region.

[8][3] In November 2012, during the aftermath of the clashes, Muhammadboqir Muhammadboqirov as well as other informal leaders, including Tolibbek Ayyombekov and Yodgorshoh Muhammadaslamov, were entered, at the request of the Tajik government, into ICPO-INTERPOL's database of wanted persons.

His daughter Bargigul Muhammadboqirova, who is a medical student at Saint Petersburg State University, claimed to have identified signs of poisoning, though a source in the hospital told Radioi Ozodi that he was simply suffering from a case of sinal inflammation.

[12][13][1] Announcing his participation in the protests, Muhammadboqirov said:[14] “The lawlessness, injustice, corruption, abuse of office, violation of every human right, freedom of speech, and freedom of the press has provoked me, a lone citizen of Tajikistan, into protesting against state employees.”In an analysis of the situation made by some media outlets, the start of the Russian invasion of Ukraine in February 2022 caused international attention to shift away from Tajikistan, which the government saw as an opportunity to increase its control over Badakhshan.

[1][15] Against this backdrop, Rizo Nazarzoda, the mayor of Khorugh, demanded that Muhammadboqirov surrender himself to the authorities, accusing him of having attacked Badakhshan education official Lutfulloh Navruzov.

Azam Tolezoda, deputy head of the Department of Internal Affairs of Badakhshan region, claimed that vehicle inspectors had only fired a warning shot to make Muhammadboqirov stop his car.

[3] A source in the interior ministry of Tajikistan reportedly told Pamir Daily News that the video was later shown to Emomali Rahmon by First Deputy Minister of Internal Affairs Abdurrahmon Alamshohzoda.

[24][25] Describing his role in the killings at a meeting with authorities of Khatlon region, Tajik president Emomali Rahmon stated:[26]“I gave the order to open fire!”Munavvar Shanbiyev, Amriddin Alovatshoyev, and Tolibbek Ayyombekov, meanwhile, were arrested and sentenced to life imprisonment.

Only Yodgorshoh Muhammadaslamov managed to avoid either fate, due to having retired from politics a few years prior and now living the life of an ordinary citizen in Porshinev.