The Vatican refers to the seat of the Catholic Church in Rome.
The term "Vatican" actually refers to the "Holy See" or Holy Seat of the Catholic church, as well as the official seat of the Pope. It is also the reference point for communion, and the central point of reference for the church everywhere.
Season One Edit
In Fated, Catherine learns of a treasonous plot by Diane to have her son Bash legitimized by the Vatican and change the line of succession.
In For King and Country, Mary tells Catherine and Henry that she will marry Bash only if he is legitimized and made the next King of France. Later Catherine tells Henry of Diane's plot, and they realize that the Pope would have to annul their marriage which would make their children illegitimate.
In Sacrifice, Henry has his Queen imprisoned in the tower while he goes off to Rome to speak with the Vatican about legitimizing Bash.
In Inquisition, while Catherine is being held in the tower on suspicion of adultery, her cousins Pierto and Francesca come to help her, and tell her that their family has put it's considerable weight on the Vatican and the Pope against annulling Catherine and Henry's marriage.
In The Consummation, with Mary stuck deciding on whether marrying Bash or Francis, Catherine gives Mary a "letter" from the Vatican supposedly with news about Bash's legitimization and helps her decide who she wants to marry.
In Liege Lord, Mary discovers that her mother and Catherine put a secret clause into her marriage contract that would give Scotland to France if she dies without an heir. Later Mary blackmails Catherine by threatening to reveal Henry's madness to the Vatican and every Noble to reveal that France is vulnerable and ready to take; unless she hands over the contract.
Season Two Edit
In Terror of the Faithful, Representatives from the Vatican are spreading terror in the villages; after Francis signs an edict forcing all to publicly declare their faith. Later Francis is threatened by a Protestant leader to either expel the Vatican which is spreading terror in France to the Protestants due to the edict; or else die along with many Catholics from hidden gunpowder which will be ignited unless the King complies. However Francis is reluctant since the Vatican gives him and Mary their power as King and Queen, and without the Vatican's blessing their rule would cease.
Season Three Edit
In No Way Out, Mary travels to Rome to visit the Vatican so that she may obtain armies and gold she needs to return to Scotland and reclaim her throne and power. To keep England in the dark; Mary refrains from telling Gideon the truth, however she tells Catherine that her trip was a success as the Vatican has agreed to help her with her quest. Later Mary gets a visit from the Vatican and they tell her that if she takes the English throne then Elizabeth will be killed; Catherine helps Mary realize that she's just a pawn in the Vatican's game to get rid of Elizabeth and put her on the throne...since they would get rid of her anyway and put a man on the throne.
After learning this, Mary is unsure as to what she should do, so she tells Gideon the truth about the Vatican's plans to kill Elizabeth.