After the battle with Lieselotte, Shiori returned to Vatican to report; Chiara Francesca, one of her most trusted friend welcomed her home at the front gate. Chiara led Shiori inside the church to meet pope Johanna and report. Before the pope, who had power and wisdom beyond anything Shiori had ever encountered, she was mentally cornered, to the point that she almost let the truth about the battle with Lieselotte slip. However, her desire to protect her friends from the hands of Index helped her stand her ground; Shiori was able to lie and told Johanna that she was the one who put both the Black Knights and Lieselotte Werckmeister out of their misery.
On the night of that same day, Shiori reunited with Sophia Measley, the creator of her artificial body and a motherly figure to her. As Shiori had been on duty away from home for a long period of time, Sophia took her to her lab for maintenance. During the process, Sophia made a joke of erasing all of Shiori's memories since they were not needed, to which Shiori strongly refused. Despite that, it was the first time they ever had a conversation like between mother and daughter. Before being shut down for further maintenance, Shiori asked Sophia to talk to her more often, to which Sophia gladly accepted.
Shiori was ordered to remain on standby while the Church process her report. During this time, she lived again in her true home and reunited with more friends, although in a different air. When she met Hieronymus of the Holy Pen, the librarian of the underground library where she lived at, he told her that she had changed much, in a good way, although he still refused to show her his face since it was his rule.
After a few days, the result of Shiori's report came in. To much of her and Chiara's astonishment, the Church decided to put her, Ursula of the Bookshelf, on trial since they were skeptical about her report of defeating both the Punishment Squad and Lieselotte so easily; even Johanna was certain that Shiori had faked her report to protect something. Shiori wrote a letter to Kakeru since her life was not guaranteed with the trial before her.
Shiori finished her letter one day before the trial and managed to send it back to Ayamegaoka. With an unrivaled strong will, she stepped into the trial ground of the Church, the final battle for freedom.
One year later (2011), Shiori returned to Ayamegaoka and reunited with Kakeru. While she said she somehow managed to quit Index unharmed, they only gave her a small amount of money to travel by train. She told Kakeru that without Index's financial support, she would only be a normal civilian, and an unemployed one at that. As such, she told him that from that point onward, she would be under his care. Kakeru agreed to look after her for the rest of his life and the two resumed their love.
After a few years, Shiori and Kakeru finally married to each other and had a son. On one day, Shiori retold her child the adventure a group of friends had undergone, hoping that the story would never be forgotten in the future.
List of events
Shiori received her mission, left Vatican and headed for Japan.
Shiori transferred into Kakeru's class.
Kukuri resurrected Shiori.
Johanna reminisced her past. Her identity of Maria Magdalene was revealed.
Johanna asked Hieronymus about his opinion on the multi-world theory.
Johanna informed Chiara of the possibility of Ursula being judged by the Vatican Catholic Council.
Sophia expressed her rage over the decision of the trial. She tried to claw Johanna's head off, but the Pope survived. Johanna explained her survival by using her view of the world in God's perspective.
Johanna resumed the talk about the multi-world theory.
Johanna appointed Chiara to send a letter, which might change Ursula's fate, to the Council. Believing that Ursula would win the trial, Sophia came to bid the Pope farewell afterwards.
Shiori returned to Ayamegaoka and reunited with Kakeru.
Shiori and Kakeru started their new life.
Shiori Satsuki went out for a picnic with her son, concluding the arc by retelling her past adventure.