Return and death
Alexei would only consent to return if his father swore that, upon return, he would not be punished, would be allowed to live quietly on his estates and to marry Afrosinya. The Tsar wrote that he would be pardoned and Alexei left for Russia with his escorts. Afrosinya remained in Venice, while Alexei reached the border of Russia on 21 January 1718. On January 31, the Tsarevich reached Moscow. At a meeting of Russian nobles in the great hall of the Kremlin, he was disinherited as Tsarevich of Russia. Alexei however was pardoned on condition he name his accomplices. However, the revealing of several damning letters and a wider circle of disaffected accomplices led Peter to determine to institute an inquisition into the reasons for Alexei's flight which was considered to be a conspiracy against the Tsar. On February 18, Alexei confessed under torture, implicated most of his acquaintances, and publicly renounced the succession to the throne in favor of his infant half-brother Peter Petrovich.
The reprisals against the Tsarevich's alleged co-conspirators were swift, unyielding, and harsh. The former Tsarina Eudoxia was dragged from her monastery and publicly tried for alleged adultery. The acquaintances of Alexei were impaled, broken on the wheel, or otherwise tortured to death. Alexei's servants were beheaded or had their tongues cut out. This not only cut off the Tsarevich from potential allies but also served to sanction the persecution of the conservative faction, which had long opposed Peter's policies.
In April 1718, fresh confessions were extorted from Alexei. This included testimony of Afrosinya, who had turned state's evidence, and reported Alexei telling her:
I shall bring back the old people and choose myself new ones according to my will; when I become sovereign, I shall live in Moscow and leave Saint Petersburg simply as any other town; I won't launch any ships; I shall maintain troops only for defense, and won't make war on anyone; I shall be content with the old domains. In winter, I shall live in Moscow, and in summer in Yaroslavl.
Despite limited evidence of existence of a conspiracy, Peter considered his son to be a confessed and dangerous traitor and submitted his case to a grand council of prelates, senators, ministers, and other dignitaries on June 13, 1718 (O.S.). The clergy, for their part, declared that Tsarevich Alexei:
"...had placed his Confidence in those who loved the ancient Customs, and that he had become acquainted with them by the Discourses they held, wherein they had constantly praised the ancient Manners, and spoke with Distaste of the Novelties his Father had introduced."
Yet as they declared this to be a civil rather than an ecclesiastical matter, the clergy left the decision to the Tsar. At noon on June 24 (O.S.), the temporal dignitaries – the 127 members of both the Senate and magistrates that comprised the court – declared Alexei guilty and sentenced him to death. Peter ordered further interrogations, possibly to uncover broader dissent or involvement.
On June 19 (O.S.), the weak and battered Tsarevich was subjected to twenty-five strokes with the knout, and then, on June 24 (O.S.), to fifteen more. On June 26 (O.S.), Alexei died in the Peter and Paul fortress in Saint Petersburg, two days after the senate had condemned him to death for conspiring to rebel against his father by provoking a popular revolt and armed intervention of his sister-in-law's husband, Emperor Charles VI.