I ask as a Medievalist who’s well familiar with the amount that the legends surrounding missionary work get distorted, but how much does this play into even modern views of Catholicism in Japan? How many missionaries were successful, and how many were notably martyred? Were Catholic missionaries greeted similarly in Early Modern Japan as they were in other states?
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Silence is a fairly solid depiction of the last stage of Early Modern Jesuit presence in Japan -- its central European character, the Portuguese Jesuit apostate Sebastiao Rodrigues, is a fictionalized counterpart to the Italian Jesuit apostate Giuseppe Chiara. Chiara's voyage to Japan and his captivity there as well as his subsequent apostasy and continued life in Japan are attested to in contemporary Japanese sources as well as Jesuit sources. The particulars of Chiara's presence in Japan differ from the fictional Rodrigues in a number of ways, but in theory both Chiara and his fictional counterpart were Jesuits attempting to enter Japan after Tokugawa Iemitsu's expulsion of all Portuguese and exclusion of all but a handful of Europeans in 1639. Chiara entered Japan with three other Jesuits in 1643, seeking to inquire after the fate of a missing Jesuit administrator; the men were quickly captured and all four Jesuits then apostatized under torture. The novel and film also introduce the wrinkle that Chiara's counterpart Rodrigues is a former student of the administrator he seeks, the historical Jesuit apostate Cristovao Ferreira. This dynamic ups the stakes, and increases the drama of the confrontation between the older Jesuit and his younger counterpart, but as far as I can tell it's also an invention of the original novel. The fictional Rodrigues character, entering Japan in 1640, is freed up to see and do things in Japan that Chiara as far as we know never did, with the fictional figure of Garrpe as his foil -- I've had a friend float that they symbolize two sides of the Society of Jesus, with Rodrigues as the mystic and Garrpe as the practical side, but idk about that.
The historical Ferreira became the Jesuit Vice-Provincial of Japan in 1632, in the midst of a renewed outburst of persecutions under the joint governors of Nagasaki. By October 1633, upwards of fifty Catholic religious (a mix of European and Japanese Jesuits, Dominicans, Franciscans, and Augustinians) and their associates had been killed following torture. Ferreira apostatized under torture. In the process of formally renouncing his faith Ferreira became a valuable rhetorical tool to demoralize remaining lay Christians and discourage the Society of Jesus from sending any more missionaries. Conflicting information about Ferreira's fate began to circulate outside Japan, and a number of Jesuit information-gathering efforts were subsequently extended into Japan. The controversy of Ferreira's apostasy and the muddle of information surrounding his fate resulted in multiple attempts to enter Japan and convince Ferreira to resume his Christian faith, including the incursion made by the four Jesuits in 1643. Ferreira's presence in Nagasaki and Edo, his sworn apostate status, his having taken a Japanese name and a Japanese wife, his nominal employment as a translator, and his supposed authorship of anti-Christian texts all appear in Japanese and Dutch sources -- though Ferreira's disposition in captivity, his psychological state, and the extent to which he voluntarily participated in the persecution of other Christians are all more debatable. So, pretty much the ideal blank check for a novelist or a screenwriter wanting to explore an interesting gap in our knowledge of a historically significant and troubled individual. So far, so good.
(Re. torture: Jesuit reports of the methods employed in anti-Catholic persecution in this era are corroborated by accounts given by Dutch Protestants, individual who had their own reasons to be severely skeptical of Catholicism and its clergy, so it seems unlikely to be 100% pure Catholic mythmaking at play. The methods of torture and execution represented in these Dutch accounts as well as Jesuit accounts are generally reflected in the film -- crucifixion, burning at the stake, burning with boiling water, beheadings, beatings, and drownings. The use of suspension in the pit as a method of torture is corroborated in the notes of Inoue Masashige; the pit is attested in Jesuit sources but later appears in the works of French Huguenot turned Dutch trader François Caron. Other methods of torture described in Dutch trader accounts, such as flaying and sexual violence, are less represented in official Jesuit accounts of martyrdom and are absent from the film.)
However by dint of its focus on the tail-end of Jesuit presence in Early Modern Japan and the fate of the last European Jesuits known to reside there before the end of Japan's seclusion policies in the 19th century, the film doesn't necessarily give a complete image of the preceding decades or the full scope of Catholic presence in Japan. These elements are often discussed rather obliquely, but they're the necessary backdrop for why Rodrigues and Garrpe are even there, beginning with the entry of Francis Xavier in 1549. Multiple characters discuss the legacy of the Jesuit presence in the 16th century before Japan's entry into seclusion, but when the film opens in 1640 the golden age for Catholic missionary activity in Japan was already in the rear-view mirror. How successful were Catholic missionaries to Japan before the Shimabara Rebellion and the ensuing renewal of anti-Christian persecution? If we're rating success in terms of successful conversions and the number of missionaries present, the Jesuit presence in Japan certainly had high points and low points, and by the late 1630s Catholicism in Japan was definitely at a low point.
At the peak of Catholic missionary success in the 1580s, the number of Christian converts in Japan numbered around 130,000. As in China, Christian missionaries were met with intellectual curiosity as well as with a eye to political and economic advantages. Many of the first targets for Catholic proselytization weren't the humble peasants to whom the fictional Rodrigues and Garrpe minister -- conversion efforts were aimed at educated individuals with something to gain from an economic/social link to the West and enough class clout to influence their peers as well as their social inferiors. One ideal scenario, at least for some missionaries, was a kind of trickle-down conversion -- a Christian-friendly daimyo might permit (or indeed require) the individuals under their authority to participate in mass baptisms and subsequent religious education. Other higher-status converts might create still more converts by example or by spreading Christianity within their own families. This top-down approach was more or less in line with Jesuit strategies in China, and the strategy of approaching the wealthy and influential was a tried-and-true one in Europe, but the approach to missionary activity in Japan was fairly different from the tack taken in missionary work elsewhere in Asia, Africa, and the Americas, where indigenous cultures were often seen as de facto less intellectually developed and less compatible with Christianity. The Jesuits were also not the only Catholic missionaries in Japan -- nor were they the only Christians, and the Society's ongoing turf wars with Dutch Protestant traders and other Catholic religious orders that sought to gain influence in Japan stoked their reputation as potential trouble-makers. The film's discussion of Jesuits and other Christian missionaries mingling self-interest in politics and trade with their supposedly selfless spread of the Christian faith is also pretty accurate -- by 1640 a lone pair of Portuguese Jesuits would be in little position to wrangle for position with the promise of financial gain, but their better-off predecessors had involved themselves freely in trade and politics, making plenty of enemies in the process, and other factions with competing interests had been warning their own governmental allies for decades about the Jesuits' supposedly grasping, manipulative nature. The film's inquisitor's suspicion of self-interested ulterior motives on the part of the Jesuits reflects a reality of the era despite Rodrigues' protests.
For the first fifty or sixty years of Catholic missionary activity in Japan, the missionaries had achieved many of their goals -- established churches and residences for Christians, founded hospitals, baptized families and individuals, translated catechisms and other devotional materials into Japanese for educated audiences, enlisted daimyo to their cause, sent groups of aristocratic young converts as ambassadors to the Christian world. Predominantly Christian neighborhoods began to form. Japanese Christians pursued and in many cases achieved holy orders, participating in religious education at Jesuit seminaries seeded throughout Asia. And yet very little of this development managed to endure within Japan once anti-Christian shogunate policies reached critical mass; the remnants of Japanese Christianity that did remain after the violent suppressions of the 1620s and 1630s did so clandestinely or in exile. So what happened to all that growth? Churches and residences were dismantled, Christian texts were destroyed, sympathetic daimyo were disciplined or overthrown, Christian neighborhoods were raided, Japanese Christian expats were refused entry into Japan, and Japanese Christian clergy who dared to return were executed. Forced conversions suddenly lost their oomph, and reluctant converts found themselves in a position to return to the religious beliefs they preferred. All this presented some persuasive reasons for the vast majority of Christians in Japan up until that point to either reconsider their beliefs and renounce them accordingly, or to retreat into extreme secrecy. Few if any of the aristocratic patrons of Catholicism retained their faith affiliation in the face of the turmoil of the 1620s and 1630s -- the disincentives to retaining faith were many and the practical incentives like trade opportunities with the West were strongly diminished from what they'd been like in the preceding century.