Beginning in August 1980 Ağca began criss-crossing the Mediterranean region, changing passports and identities, perhaps to hide his point of origin in Sofia, Bulgaria. He entered Rome on May 10, 1981, coming by train from Milan.
According to Ağca's later testimony, he met with three accomplices in Rome, one a fellow Turk and two Bulgarians, with operation being commanded by Zilo Vassilev, the Bulgarian military attaché in Italy. He said that he was assigned this mission by Turkish mafioso Bechir Celenk in Bulgaria. Le Monde diplomatique, however, has alleged that the assassination attempt was organized by Abdullah Çatlı "in exchange for the sum of 3 million marks", paid by Bechir Celenk to the Grey Wolves.
According to Ağca, the plan was for him and the back-up gunman Oral Çelik to open fire in St. Peter's Square and escape to the Bulgarian embassy under the cover of the panic generated by a small explosion. On May 13 they sat in the square, writing postcards waiting for the Pope to arrive. When the Pope passed, Ağca fired several shots and critically wounded him, but was grabbed by a nun and several other spectators and prevented from finishing the assassination or escaping. Four bullets hit John Paul II, two of them lodging in his lower intestine, the others hitting his left hand and right arm. Two bystanders were also hit by stray assassin's bullets; Ann Odre, of Buffalo, New York, was struck in the chest while Rose Hill, of Jamaica, was slightly wounded in the arm. Çelik panicked and fled without setting off his bomb or opening fire.
Although Ağca had been quoted as saying that "to me [the Pope] was the incarnation of all that is capitalism", and attempting to murder him, Ağca developed a friendship with the pontiff. In early February 2005, during the Pope's illness, Ağca sent a letter to the Pope wishing him well and also warning him that the world would end soon.
Ağca himself has given multiple conflicting statements on the assassination at different times. Attorney Antonio Marini stated: "Ağca has manipulated all of us, telling hundreds of lies, continually changing versions, forcing us to open tens of different investigations". Originally Ağca claimed to be a member of the Marxist Popular Front for the Liberation of Palestine (PFLP), but they denied any ties to him.
Then KGB Director Yuri Andropov, was convinced that the Pope John Paul II’s election was the product of an Anglo-German conspiracy orchestrated by Zbigniew Brzezinski to undermine Soviet hegemony in largely Catholic Poland and ultimately to precipitate the collapse of the entire Soviet Union. The Pope’s announcement of a pilgrimage to Warsaw fueled Andropov’s apprehension, with Andropov issuing a secret memorandum to Soviet schoolteachers:
The Pope is our enemy. . . . Due to his uncommon skills and great sense of humor he is dangerous, because he charms everyone, especially journalists. Besides, he goes for cheap gestures in his relations with the crowd, for instance, [he] puts on a highlander’s hat, shakes all hands, kisses children, etc. . . . It is modeled on American presidential campaigns. . . . Because of the activities of the Church in Poland our activities designed to atheize the youth not only cannot diminish but must intensely develop. . . . In this respect all means are allowed and we cannot afford sentiments.
Ali Agca had made several trips to Sofia, Bulgaria, and stayed in a hotel favored by the Bulgarian (DS). In Rome he had also had contacts with a Bulgarian agent whose cover was the Bulgarian national airline office. Soon after the shooting, Sergei Antonov, a Bulgarian working in Rome for Balkan Air, was arrested based on Ağca's testimony and accused of being the Bulgarian agent who masterminded the plot. In 1986, after a three-year trial, he was found not guilty. According to Paul Henze (1985), he later stated that in Sofia, he was once approached by the Bulgarian Secret Service and Turkish mafiosi, who offered him three million German mark to assassinate the Pope.
Columnist Eric Margolis commented that Ağca was an ideal candidate, because while Ağca appeared to be a Turkish neo-fascist he was really being run by KGB via its Bulgarian subordinates, in a classic false flag operation. The Bulgarians chose Ağca to supply themselves with plausible deniability; choosing a member of the Grey Wolves that had been involved with the local KGB in drug smuggling routes through Bulgaria to Western Europe would distance themselves because of the implausibility of the link.
According to Ferdinando Imposimato, an Italian prosecutor in charge of the assassination investigation, Ağca has confirmed the KGB and the Bulgarian involvement during their many private conversations in 1997-2000, tying it to the mysterious 1998 murder of Colonel Alois Estermann, a Swiss Guard. Ferdinando Imposimato has alleged a link with the East German secret service.
According to Italian newspaper Corriere della Sera, documents recovered from former East German intelligence services confirm the 1981 assassination attempt against Pope John Paul II was ordered by the Soviet KGB and assigned to Bulgarian and East German agents with the Stasi to coordinate the operation and cover up the traces afterwards, however, Markus Wolf, former Stasi spy-master, has denied any links, and claimed the files had already been sent in 1995 .
In March 2006, the controversial Mitrokhin Commission, set up by Silvio Berlusconi and headed by Forza Italia senator Paolo Guzzanti, supported once again the Bulgarian theory, which had been denounced by John Paul II during his travel to Bulgaria. Senator Guzzanti claimed that "leaders of the former Soviet Union were behind the assassination attempt", alleging that "the leadership of the Soviet Union took the initiative to eliminate Pope John Paul" because of his support for Solidarity, relaying "this decision to the military secret services" (and not the KGB). The report's claims were based on recent computer analysis of photographs that purported to demonstrate Antonov's presence in St Peter's Square during the shooting and on information brought by the French anti-terrorist judge Jean-Louis Bruguière, a controversial figure whose last feat was to indict Rwandese president Paul Kagame, claiming he had deliberately provoked the 1994 Rwandan Genocide against his own ethnic group in order to take the power . According to Le Figaro, Bruguière, who is in close contacts as well with Moscow as with Washington DC, including intelligence agents, has been accused by many of his colleagues of "privileging the reason of state over law."
Both Russia and Bulgaria condemned the report. ""For Bulgaria, this case closed with the court decision in Rome in March 1986," Foreign Ministry spokesman Dimitar Tsanchev said, while also recalling the Pope's comments during his May 2002 visit to Bulgaria. Senator Guzzanti said that the commission had decided to re-open the report's chapter on the assassination attempt in 2005, after the Pope wrote about it in his last book, Memory and Identity: Conversations Between Millenniums. The Pope wrote that he was convinced the shooting was not Ağca's initiative and that "someone else masterminded it and someone else commissioned it". The Mitrokhin Commission also claimed current Prime minister of Italy, Romano Prodi, was the "KGB's man in Italy". At the end of December 2006, Mario Scaramella, one of the main informer of senator Guzzanti, was arrested and charged, among other things, of defamation. Rome's prosecutor Pietro Salvitti, in charge of the investigations concerning Mario Scaramella, cited by La Repubblica, showed that Nicolò Pollari, head of SISMI, the Italian military intelligence agency and indicted in the Imam Rapito affair, as well as SISMI n°2, Marco Mancini, arrested in July 2006 for the same reason, were some of the informers, alongside Mario Scaramella, of senator Paolo Guzzanti. Beside targeting Romano Prodi and his staff, this "network", according to Pietro Salvitti's words, also aimed at defaming General Giuseppe Cucchi (current director of the Cesis), Milan's judges Armando Spataro, in charge of the Imam Rapito case, and Guido Salvini, as well as La Reppublica reporters Carlo Bonini and Giuseppe D'Avanzo, who discovered the Yellowcake forgery affair . The investigation also showed a connection between Scaramella and the CIA, in particular through Filippo Marino, one of Scaramella's closest partners since the 1990s and co-founder of the ECPP, who lives today in the US. Marino has acknowledged in an interview an association with former and active CIA officers, including Robert Lady, former CIA station chief in Milan, indicted by prosecutor Armando Spataro for having coordinated the abduction of Abu Omar, the Imam Rapito affair .
Some people, notably Edward S. Herman, co-author with Frank Brodhead of The Rise and Fall of the Bulgarian Connection (1986), and Michael Parenti, felt Ağca's story was dubious, noting that Ağca made no claims of Bulgarian involvement until he had been isolated in solitary confinement and visited by Italian Military Intelligence (SISMI) agents. On September 25, 1991, former CIA analyst Melvin A. Goodman (now Senior Fellow at the Center for International Policy) revealed that his colleagues, following hierarchical orders, had falsified their analysis in order to support the accusation. He declared to the US Senate intelligence committee that "the CIA hadn't any proof" concerning this alleged "Bulgarian connection" Neither the Severino Santiapichi court, nor the investigation by judge Franco Ionta, found evidence that that SISMI planted Ağca's story. A French lawyer, Christian Roulette, who authored books blaming Western intelligence agencies for the assassination attempt, testified in court that documentary evidence he referred to actually did not exist.
The Bulgarian secret services have always protested their alleged involvement and argued that Ağca's story was an anti-Communist plant placed by the Grey Wolves, the Italian secret service, and the CIA - all three of whom had cooperated in NATO's secret Gladio network . Gladio was at the time involved in Italy's strategy of tension, also followed in Turkey by Counter-Guerrilla, the Turkish branch of Gladio. The Pope's assassination would hereafter have taken place in this frame. Edward Herman has argued that Michael Ledeen, who was involved in the Iran-Contra Affair and had alleged ties to the Italian P2 masonic lodge also linked to Gladio, was employed by the CIA to propagate the Bulgarian theory . Indeed, the Monde diplomatique alleged that Abdullah Çatlı, a leader of the Grey Wolves, had organized the assassination attempt "in exchange for the sum of 3 million German Marks" for the Grey Wolves . In Rome, Catli declared to the judge in 1985 "that he had been contacted by the BND, the German intelligence agency, which would have promised him a nice sum of money if he implicated the Russian and Bulgarian services in the assassination attempt against the Pope". According to colonel Alparslan Türkes, the founder of the Grey Wolves, "Catli has cooperated in the frame of a secret service working for the good of the state" .
Another theory, described in the Gordon Thomas's book Gideon’s Spies: Mossad’s Secret Warriors, rejects the KGB, Turkish and Bulgarian connections. According to Thomas, a British specialist on intelligence, the assassination was ordered by Iranian Ayatollah Khomeini as a first act of Jihad, the Muslim holy war, against Christianity and the Occident. This theory is based on the following elements: The Grey Wolves organization was pro-Iranian; Mehmet Ali Ağca was trained in Iran; the text of a 1979 letter sent to the press by Mehmet Ali Ağca just after he killed a Turkish journalist used formulas such as "Supreme Commander of the Crusaders" that are directly taken from Khomeini's style, while Ağca is nearly illiterate. The 1983 Pope visit to his aggressor in jail was aimed to confirm this theory, just uncovered by the Israeli intelligence agency.
Finally, Jack Chick claims that Pope John Paul II, a good Communist for many years, engineered his own assassination in 1981 to shame Islam into warming relations with the Vatican, since the would-be killer was a Muslim. This was because the Catholic Church's Vatican Islam Conspiracy to create Islam and make its leader Muhammed their ultimate warrior backfired against them.
On March 31, 2005, just two days prior to the Pope's death, Ağca gave an interview to the Italian newspaper La Repubblica. He claimed to be working on a book about the assassination attempt. La Repubblica quoted Ağca claiming at length that he had accomplices in the Vatican who helped him with the assassination attempt, saying "the devil is inside Vatican's wall". He also said:
Emanuela Orlandi, the daughter of a Vatican employee, disappeared at age 15 on June 22, 1983. Anonymous phone calls offered her release in exchange for the release of Ağca. Archbishop Paul Marcinkus was alleged to be part of the kidnapping, although no charges were ever laid.
A week after this interview, Associated Press reported Ağca denying having made such claims.