The prison of the Trubetskoy Bastion, which had existed in the Peter and Paul Fortress since the tsarist times, came under the control of the communists after the October Revolution. On the night of October 25 to 26, ministers of the Provisional Government, arrested in the Winter Palace during the coup, were imprisoned there.

In December 1917, the Trubetskoy Bastion prison was transferred to the system of Cheka prisons. Hundreds of prisoners were held here: participants in the Junker uprising organized by the Committee for the Salvation of the Motherland and the Revolution, members of the "Union for the Defense of the Constituent Assembly," and the leaders of the Cadet party declared "enemies of the people" at the end of 1917. Officially, by order of the People's Commissariat of Justice dated March 7, 1918, the prison was closed, and all prisoners were transferred to the "Crosses" and the House of Preliminary Detention. However, from May 1918, prisoners were again held here — suspects in opposing the new government, as well as hostages during the Red Terror, participants in the Kronstadt uprising of 1921, and many others.

In late summer — early autumn 1918, the Petrograd Cheka arrested 6,229 people. On August 30, the head of the city Cheka, M. S. Uritsky, was assassinated in Petrograd, and an attempt was made on V. I. Lenin in Moscow. In response, the communist authorities immediately executed 512 hostages. After this, on September 5, the Council of People's Commissars of the RSFSR issued an official decree "On the Red Terror," and on September 6, lists of prisoners to be executed in case of new assassination attempts were published in the press.

Memoirs of contemporaries indicate that the fortress was a place of executions and burial of the executed. This was written about by prison inmates A. I. Kalpashnikov and A. D. Zinoviev, and by I. M. Lyapin, a member of the troika conducting the Red Terror in Petrograd. In the diary of Z. N. Gippius and the memoirs of D. S. Likhachyov, it is recorded that starting from September 1918, gunshots were heard from the Peter and Paul Fortress. According to typographers’ testimonies, executions were carried out near the walls of the Nikolskaya Curtain and the Golovkin Bastion. Numerous sources also testify that four grand dukes were executed in the Peter and Paul Fortress in January 1918. Officially, these executions were justified in the press as a response to the murder of Rosa Luxemburg and Karl Liebknecht in Germany (although this occurred after the execution of the grand dukes). According to the memoirs of Princess O. V. Paley, the execution was carried out on the territory of the Mint Yard near the fortress wall. According to one fortress worker’s recollections, after the Junker uprising, they were transferred to the Trubetskoy Bastion prison, but some tried to escape on the way, and the young men were shot, including in sheds on the northern part of the island where they tried to hide.

Executions and subsequent burials took place on the territory near the Golovkin Bastion. At the beginning of the century, this area indeed belonged to the Mint Yard — there were wood sheds and warehouse buildings. Thanks to these structures and the fact that the Kronverk shore was planted with trees, this place was hidden from the public eye, which was very suitable for carrying out killings. It is not exactly known whether all those executed were prisoners of the Trubetskoy Bastion prison. According to executioner I. M. Lyapin, some were specially brought to the Peter and Paul Fortress for execution.

In 1924, the Trubetskoy Bastion prison was finally closed and turned into a museum. Initially, it was a branch of the Museum of the Revolution, and since 1954 — the State Museum of the History of the City. The site of the executions near the Golovkin Bastion remained under the jurisdiction of the NKVD-OGPU military garrison for some time, then it was transferred to other institutions. During all this time, various land and construction works were carried out there, during which part of the burials was disturbed.

At least since the late 1980s, human remains, as well as spent cartridges and bullets, have been found on the territory of the Peter and Paul Fortress. For example, in 1989, during construction work near the western facade of the Golovkin Bastion at a depth of about one meter, four skeletons were found. The remains were extracted and placed in the collections of the Museum of the History of Saint Petersburg. However, no forensic medical examination was conducted, and this information was not publicized.

In March 2007, during earthworks between the Kronverk Channel and the Golovkin Bastion at a depth of about two meters, a burial of two or three people was discovered. Construction work was suspended, and the found remains were reported to the Petrograd District Police Department. The search team "Ingria" of the History Faculty of St. Petersburg State University conducted an investigation of the burial site, during which fragments of military uniforms from 1907–1916 (greatcoat, officer’s tunic, and others) and spent rifle cartridges were found. Together with the 1989 finds, they were sent for examination to the forensic medical department of the Bureau of Forensic Medical Examination. According to the forensic experts’ conclusion, the remains belong to men aged 20–60 with gunshot wounds to the head and chest; the time the remains spent in the ground was over 50 years, and "the location of the found remains allows with a high degree of probability to assert that the buried are part of a larger burial." Historians suggested that the pit contained the remains of junkers or officers executed in late 1917 — early 1918. Despite this, the museum and city authorities kept silent on the matter.

Contrary to protests from members of the Council for the Protection of Cultural Heritage under the Government of Saint Petersburg and public representatives, construction work on the territory of the presumed necropolis continued in 2009 — a parking lot was created near the Kronverk Curtain, and a road began to be laid along the Golovkin Bastion. During these works, on December 20, 2009, human bones were found about one meter deep, 18 meters from the western facade of the Golovkin Bastion. This discovery caused a great public outcry. An interdepartmental working group was created to study it, including representatives of the State Museum of the History of Saint Petersburg, the Hermitage, the Institute of the History of Material Culture of the Russian Academy of Sciences, and the All-Russian Society for the Protection of Historical and Cultural Monuments. Earthworks were initially stopped but soon resumed despite being against the law. Nevertheless, a team led by researcher V. I. Kildyushevsky conducted an investigation of the burial. They found the remains of 16 people with clear signs of violent death, in particular, bullet holes in the occipital parts of the skulls. A large number of various items were also found, primarily fragments of clothing (civilian and military), bullets, and spent cartridges. Among the killed were one woman and one person with a leg amputated during life. The human remains were transferred to the Bureau of Forensic Medical Examination of the Leningrad Region, where a group of experts led by Professor V. L. Popov examined them. Alongside the search, research work was conducted to establish the identities of the deceased. A series of anthropological, forensic medical, and genetic examinations were carried out, and archival searches were conducted. Through joint efforts of forensic experts and historians, it was established that these were the remains of people executed on December 13, 1918, by the Cheka’s decree against counter-revolution at the Union of Communes of the Northern Region in connection with the so-called "Doctor Kovalevsky case": a list of 16 executed was found in the newspaper "Petrogradskaya Pravda," including one woman and one disabled man. Later, genetic testing involving descendants confirmed the identification of the legless man — Fleet Major General A. N. Rykov. Thus, the female remains most likely belong to V. V. Shulgina, sister of Major General B. V. Shulgin.

In June–July 2010, archaeological search work continued over an area of more than 1,200 square meters near the western facade wall of the Golovkin Bastion. As a result, V. I. Kildyushevsky’s expedition discovered six more burials totaling over 90 people, including five women. All work carried out in 2009–2011 was funded by the museum, partly on a voluntary basis. However, due to lack of funding, the search work was soon interrupted.

Archaeological research of the burial resumed only in October 2013, when funds were allocated from the Saint Petersburg budget (after numerous appeals by public activists). This time, an area of 900 square meters north of the road laid in 2009 to the parking lot near the Kronverk Curtain of the Peter and Paul Fortress was investigated. Archaeologists found four burials with remains of about 50 executed people. Thus, in total, the eleven discovered burials contained remains estimated at between 160 and 200 people.

The discovered burials can be divided into two groups: actual execution pits and places of reburial of bones, which were carried out much later than the executions — usually small graves completely lacking personal items made of precious metals (likely removed when the remains were found). The latter are the majority. Experts suggest these can be dated to the 1920s, 1930s, and 1940s, when workers found human remains during land and construction works.

The museum repeatedly appealed to the prosecutor’s office with requests to initiate a criminal case, but the Investigative Committee of the Russian Federation for Saint Petersburg refused to open a case. This decision was justified by the "expiration of the statute of limitations," meaning there were no procedural grounds. Meanwhile, as researchers point out, identification of remains at state expense can only be conducted if a criminal case is opened. Since the criminal case issue remains unresolved, the storage of remains and other finds uncovered during the excavation is temporarily carried out by the Museum of the History of Saint Petersburg, although the museum lacks proper conditions for adequate storage.

In 2014 and 2015, the museum and city authorities intended to continue excavations over an area of 3,000 m². However, these plans were never realized. Eventually, the museum and city leadership announced the completion of archaeological work. However, independent historians note that many skeleton fragments have not been found, and many areas (including the site of the new road) have not yet been investigated.

In 2014, researcher A. Ya. Razumov published a preliminary list of 502 people presumably executed in the Peter and Paul Fortress. In 2017, anthropologist D. V. Pezhemsky, who studied the remains, hypothesized the identification of the remains of the last military minister of the Russian Empire, General M. A. Belyaev.

In 2004, in the Grand Ducal Burial Vault, on the initiative of the rector of the Peter and Paul Cathedral A. N. Fyodorov, a memorial plaque was installed dedicated to the memory of the four grand dukes executed. This is the only commemorative sign marking the murders in the Peter and Paul Fortress.

On March 5, 2008, writer and honorary citizen of Saint Petersburg D. A. Granin sent a letter to Governor V. I. Matvienko proposing to install a memorial sign at the site where human remains were found near the Golovkin Bastion. However, in response, Vice-Governor S. B. Tarasov stated that the facts of executions in the Peter and Paul Fortress lack documentary confirmation and also referred to the fact that changes to the Peter and Paul Fortress, a Russian cultural heritage site, allegedly contradict the law. Several activists pointed out that both these statements are incorrect.

In 2012, historian A. D. Margolis spoke in favor of installing a memorial sign at the necropolis site and reburial of all previously found and extracted remains there. He also proposed creating an exhibition dedicated to the Red Terror in the Peter and Paul Fortress Museum.

In 2018, the issue of installing a monument was again repeatedly raised by the city ombudsman A. V. Shishlov within the framework of implementing the "Concept of State Policy for Commemorating Victims of Political Repressions." A proposal was also voiced to reinter the remains at the Cemetery of the Victims of January 9, where repressed people were secretly buried during the Soviet era. A. D. Margolis did not support this idea. Ultimately, the Saint Petersburg Committee for Culture decided to create a memorial sign at the execution site.

Nevertheless, every September on the Day of Remembrance for the Victims of the Red Terror, mourning events are held at the necropolis site. In 2015, during these events, a temporary installation-monument was set up in the form of a rolled iron grille and stakes with plaques indicating the number of people killed at the execution pits. In 2018, on the 100th anniversary of the start of the Red Terror, the leadership of the City History Museum for the first time laid flowers at the bastion. Later, a row of 120 human figure silhouettes symbolizing the people killed here was installed along the wall, each with a lantern holding a candle around its neck.

Sources:

https://ru.wikipedia.org/wiki/Некрополь_Красного_террора_в_Петропавловской_крепости