Flavia met with the fifth incarnation of the Doctor when Borusa summoned the Doctor's other selves to the Death Zone. She was sympathetic towards him, letting him in the Lord President's room and talking to the guards for him. Following Borusa's defeat and entombment in the Dark Tower, the High Council granted Flavia the authority to make the Doctor President of the High Council. The Doctor used his emergency powers to put Flavia in charge, appointing her Acting President until he returned. He then escaped from his homeworld of Gallifrey, evading the responsibility the office of Lord President. (TV: The Five Doctors)
In her first term as President, Flavia was "pitched into the Presidency when Borusa vanished and the Doctor absconded". (PROSE: The Eight Doctors) Flavia was later deposed in favour of the political non-entity Niroc after allegations were created that she had not been legitimately elected to the Presidency. The Celestial Intervention Agency wanted a President they could control more easily, to conceal the recent theft of important data from the Matrix. The Doctor was put on trial during this period. A Committee of Inquiry was opened into the trial. This was due to the actions of the Eighth Doctor and a temporal duplicate of the Sixth Doctor (the latter was created when the Valeyard tried to "force" an alternate timeline where the Sixth Doctor was found guilty and executed). Although the Sixth Doctor's temporal duplicate eventually ceased to exist, he lasted long enough to testify at his future self's inquiry. The Eighth Doctor awakened Borusa to quell the riots while the Sixth Doctor fought the Valeyard and the Master in the Matrix. (PROSE: The Eight Doctors; TV: The Trial of a Time Lord: The Ultimate Foe)
Flavia later learnt the Eighth Doctor was visiting his past seven selves for unknown reasons, bypassing all usual security protocols preventing such interaction. Flavia, despite the protests of the unscrupulous Time Lord Ryoth, decided to allow these visits to continue until they were proven to be a danger to Gallifrey. Once the visits were concluded, Flavia reflected that she wished the Doctor well in his future adventures. (PROSE: The Eight Doctors)
Conflicting accounts existed as to the manner in which Flavia's political career ended. At issue was whether Romana II had directly succeeded Flavia, or if there had been an intervening president.
Some sources held that Romana II simply contested Flavia for the presidency and won. (PROSE: Happy Endings) However, there was evidence of an intervening President. Irving Braxiatel suggested another President ruled in an interim term, and that they had been male. (AUDIO: Lies) Romana herself recalled only that she had invoked a so-called "right of challenge" against her predecessor, just as Darkel later challenged her, (AUDIO: Insurgency) after she was "asked to become President" following "the coup that overthrew Flavia's inauspicious reign" despite her lack of political experience. (AUDIO: Lies)
The character of Flavia filled in for that of Thalia, who had appeared in the earlier story, Arc of Infinity. The production team decided not to simply recast the role using the excuse of regeneration and made up a new character.