In the Season 1 finale, Gutierrez returns to Rome a changed man after the Kurtwell investigation, prompting the pope to make a decision about the archbishop's fate. Meanwhile, Father Tomasso gets a promotion; and Lenny makes an unexpected change in travel plans and policy after learning about a possible reconciliation.
A threat of blackmail is among the obstacles facing Gutierrez in New York during his investigation of Archbishop Kurtwell. Meanwhile, Lenny and Mary are reminded of an important moment from the past as the pope could lose something in the present.
Sofia returns to the Vatican and encourages the pope to make Africa his first trip abroad to mark the 30th anniversary of Sister Antonia's "Village of Goodness." Meanwhile, Lenny gets a boost from a visit by a beloved writer, but he and Mary feel the sting of a shared loss.
A would-be priest's suicide sends Voiello into damage-control mode and searching for new paths to Lenny's downfall. Meanwhile, a potential family reunion proves to be a distraction for Lenny, but presents a moral dilemma for Sister Mary; and Dussolier declares his desire to go back to Honduras in the unsettling aftermath of a social gathering in Rome.
Gutierrez moves out of Vatican City and prepares to begin his mission abroad as a newly minted cardinal. Meanwhile, Lenny's first meeting with Italy's progressive prime minister is a contentious one; Dussolier is shocked by the pope's guidelines for new priests; Voiello fields questions about Tonino's disappearance; and Ester's prayers are answered.
Rumors of a scandal are manufactured by Voiello to undermine the pope. Meanwhile, Lenny and Andrew reminisce about the past; and Lenny's address to the College of Cardinals in the Sistine Chapel won't be put off any longer.
A burial for a nun's sister at the Vatican is arranged by Lenny; Voiello finds a use for Ester in a blackmail plot; Lenny finally reaches a decision on how to handle a sex-abuse case in New York; the Greenland prime minister visits Rome; a shepherd claims to perform miracles.
Voiello charts a new course in the fallout from the pope's first public homily after it sows confusion, doubt and fear among the clergy, laity and press. Meanwhile, Lenny taps Sister Mary to outline his vision at a press conference; a woman standing alone in St. Peter's Square catches the pontiff's eye; and Gutierrez's private conversations with Lenny may be compromised by a personal shortcoming.
Lenny meets with Cardinal Spencer in anticipation of his first public appearance, but their reunion doesn't turn out the way he planned. Meanwhile, the Vatican's marketing director is surprised by the new pope's desire to remain anonymous; Sister Mary rehashes the past with an old friend of Lenny's from the orphanage; and the faithful flock to St. Peter's Square for their first glimpse of Pope Pius XIII.
In the premiere of a ten-part miniseries following the reign of Pope Pius XIII, aka Lenny Belardo, the first American pontiff, Vatican protocol and, it seems, the Catholic Church, mean little to Belardo, who hires the nun who raised him at an orphanage to be his main adviser and whose iconoclastic behavior irks the cardinals who resent his ascension.