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With the retreat of Russian forces from Kherson this month, new evidence of gruesome atrocities against civilians has become visible (link). A very important question arises: What organization and what commanders have directed this campaign of atrocity, murder, rape, mutilation, torture, and abduction? Is there good investigative reporting on where orders for these unspeakable atrocities and crimes against humanity are coming from? 
Any list of possible suspects in ordering and committing systemic and horrific atrocities in Kherson and other Ukraine locations will certainly include these potential actors: rogue low-level occupation units, mid- to high-level military commanders, the Wagner Group and its presumed commander, Dmitri Utkin, forces commanded by Chechen militia leader Ramzan Kadyrov, and Putin's secret security serve, the FSB. It goes without saying that Vladimir Putin bears ultimate responsibility for these atrocities, since he knows full well that Russian forces are committing these horrendous acts, and we can therefore infer either explicit or implicit consent on his part. But we still need to know more about the organizations and commanders who are directing this campaign of deliberate atrocity against civilians in Ukraine.
A leading candidate is the Russian security service, the FSB, which is the successor to Stalin's NKVD and has been enormously empowered under Putin's rule. Andrei Soldatov and Irina Borogan provide a detailed and highly concerning analysis of Putin's FSB in their 2011 book, The New Nobility: The Restoration of Russia's Security State and the Enduring Legacy of the KGB. The book provides detailed information about the organization and functions of the FSB, as well as informed estimates of its overall size (more than 200,000; p. 2). The book also provides a detailed historical chronology of the evolution of the FSB since Gorbachev's dissolution of the KGB in 1991. 
Soldatov and Borogan document the wide extent of extra-judicial killing in the war in Chechnya and Dagestan by the security services.
Neighboring Dagestan has seen twenty-five kidnappings since February 2009 by Memorial’s count, twelve of which resulted in the murder of victims. A week after the press conference, Sirazhudin Umarov, 32, a construction worker, was kidnapped from Qala, a Derbent district of Dagestan. On September 9 he was called to a meeting by an acquaintance named Azer, a police officer. There Umarov was captured by unidentified masked men. The following day his badly mutilated body was discovered. The security forces confirmed that he had been killed by the authorities, though they claimed he had died during an antiterrorism operation. “His face was so badly smashed from beating that I had difficulty recognizing him,” said Gulbenis Badurova, 33, his wife. “His eye was missing, and both hands had been broken.” (184)
(Soldatov's account of his own interrogation at Lefortovo Prison is chilling, and expresses the nature of the Russian police state.) 
There is a direct lineage connecting Stalin's NKVD (the primary agent of Stalin's terror and repression) and the contemporary FSB, and Soldatov makes the case that the parallels are even more striking today than they were twenty years ago. The lineage from the NKVD to the FSB is important, because the NKVD carried out horrific atrocities and massacres throughout the Stalin period: in 1940 it carried out the Katyn Forest massacre of at least 20,000 Polish army officers (prisoners of war), and in 1941 it carried out a series of massacres of political prisoners in Kiev and other locations in Ukraine (link). (Here is some background on NKVD atrocities in Ukraine in1941; link.) There is no basis for doubting that the NKVD was the author of great atrocity and evil in the 1930s through 1950s and was the primary instrument of Stalin's will throughout those decades.
It is reasonable to ask, therefore, what role FSB directors and special forces agents have played in the atrocities of torture, rape, kidnapping, and murder that have become evident in multiple locations in Ukraine recovered from Russian occupation in recent months.
In a recent article in Foreign Affairs (link) Andrei Soldatov documents the increasing role of repression that has been assigned to the FSB during Putin's rule -- including in the occupation of territory seized from Ukraine since February 2022. The conclusion that Soldatov draws is stark: the FSB is moving closer and closer to the repressive omnipresent arm of a police state that the NKVD was for Stalin:
Since the war in began, Putin’s rapidly growing security state seems to be inching closer to its Stalinist predecessor. The militarization of the FSB, its new recruitment camps, its increasingly open and brutal tactics all suggest that Putin is looking more closely at the approach of the NKVD—an agency that was forged by a totalitarian state in wartime. And the long war is what the Kremlin is priming the country for.
Here is how Soldatov describes the new focus of the FSB, both in Russia and in its war aims in Ukraine:
As Russian President Vladimir Putin’s war in enters its sixth month, a dramatic shift has occurred in the Kremlin’s security bureaucracy, and it has centered on the agency closest to Putin himself: the Federal Security Service, or FSB. When the war began, the Kremlin planned to use the FSB mainly in Ukraine, as a special operations force that would consolidate a rapid Russian conquest. According to the plan, the Russian tanks rolling into Ukraine would trigger regime change in Kyiv, and a new pro-Moscow leadership, sponsored by FSB spymasters, would take control of the country. At the time, it was the FSB’s foreign intelligence branch—the Fifth Service—that was to carry out this task. It was the only major FSB department, out of a dozen, that was directly involved in preparing for the war.
As those plans, however, Putin crafted a different, far more comprehensive mission for the FSB: it would be at the forefront of Russia’s total war effort at home as well as its intelligence operations in Ukraine. And every branch of the service would now be involved. Running the new crackdowns in are the FSB’s counterterrorism unit, its counterintelligence service, and its investigative department. Meanwhile, FSB special forces and the military counterintelligence branch are running operations targeting Ukrainian service people in occupied territories and beyond, recruiting Ukrainian agents, and processing those whom the FSB hopes to see prosecuted in show trials.
Notice that Soldatov's description in the paragraphs quoted here specifically outlines a substantial role for the FSB in occupied Ukraine, according to Putin's pre-war planning. 
My question here is a simple one: how extensive is the involvement of the FSB in the widespread and horrific atrocities that have come to light in Kherson, Bucha, and many other locations in previously occupied Ukraine? These acts of rape, murder, and torture against innocent civilians are generally attributed to "troops" in news stories, which perhaps leads the reader to imagine "rogue low-level army units"; but this is implausible. The atrocities are too widespread to reflect a few sadistic killers among the Russian army of occupation. Therefore we need to know more about the command and control of this horrific way of waging a war of terror and atrocity against civilians in Ukraine. And the world must hold Russia and its bureaucrats of atrocity accountable for their actions during this war.