Chronicles: Russia is set in early 20th-century Soviet Russia, in the aftermath of the October Revolution of 1917, and follows Nikolai Orelov, the protagonist of the comic book Assassin's Creed: The Fall and its graphic novel sequel, The Chain. In 1918, Nikolai contemplates retiring from the Assassin Brotherhood and leaving the country with his family, but agrees to perform one final mission: to recover the Precursor box, which is believed to be in the possession of the Romanov family. On the night of 16–17 July, he travels to Yekaterinburg and infiltrates the house where former Tsar Nicholas II and his family are being held, only to witness their execution at the hands of Templar agents infiltrated within the Red Army, who also seek the box. Nikolai discovers that the Tsar's youngest daughter, Anastasia, survived the massacre and has the box, which somehow links her to Shao Jun, giving her the latter's memories and abilities, which she is unable to control.[7]

Taking pity on Anastasia, Nikolai decides to take her back to the Brotherhood in the hope that they could help her. Pursued by both the Templars and the Bolsheviks, the two escape Yekaterinburg on a train headed to Kazan, arriving there in September, in the midst of the Red Army's attempt to retake the city. Nikolai leaves to find his old friend, Leon Trotsky, only to discover that the latter, believing Anastasia to be too dangerous as a symbol to be left alive, has allied with the Templars. Trotsky betrays Nikolai to the Templars, who torture him for the location of Anastasia and the Precursor box. Anastasia manages to rescue Nikolai, and together they escape Kazan by stealing a boat.

Nikolai and Anastasia sail to Moscow, where the two are separated upon meeting the other Assassins, who take Anastasia away to experiment on her and find a possible cure for her condition. Nikolai is instructed to return to the Assassins' bureau to report about his recent experiences, but overhears two Assassins talking about how Anastasia is now a living Precursor artifact and that they must extract Jun's memories from her, likely killing her in the process. Caring for Anastasia and enraged by the Assassins' lies, Nikolai decides to betray the Brotherhood to save the girl. After interrogating an Assassin, he learns that Anastasia was taken to the Kremlin, and proceeds to make his away across the city while avoiding his former Assassin brothers, who now have orders to kill him.

After infiltrating the facility where Anastasia is being kept, Nikolai rescues her and the two work together to escape back to the city. Once there, the Assassins try to kill them using a tank, but Nikolai is able to destroy it. Afterwards, Nikolai gives Anastasia false documents originally intended for his wife, providing her with a new identity, Anna Anderson, and a means to leave the country unnoticed. The two part ways, with Anastasia planning to start a new life in Germany, and believing that she will be able to keep Jun's memories under control.

Secret ending

A secret ending can be unlocked in Chronicles: Russia by inputting hidden codes found throughout all three games. The ending takes place in the modern day, where Templar agent Juhani Otso Berg meets up with the Head of Operations at Abstergo Industries, Laetitia England. Berg, who has recently studied the memories of Assassin-turned-Templar Shay Cormac to learn more about the Precursor box, presents it to England, who instructs him to take it to Dr. Álvaro Gramática in secret. Gramática claims the box to be instrumental in the success of Abstergo's Phoenix Project.