Ionius IX was crowned sometime before Imperial Year 1162, when his daughter and future heir Edelgard was born to his wife Patricia, the sister of Lord Volkhard von Arundel. He fathered a total of eleven children, though Edelgard was one of the few who bore the Crest of Seiros. Edelgard was born to one of his consorts that he met after his politically motivated sole marriage.
In 1171, he was stripped of most of his power by a group of nobles led by Duke Aegir in a coup d'etat called the Insurrection of the Seven. Amidst the upheaval, Edelgard and Patricia were taken to the Holy Kingdom of Faerghus in apparent exile by Patricia's brother, Lord Volkhard, who was also one of the key conspirators. Patricia later married King Lambert of Faerghus, and stayed behind in the Kingdom when Volkhard and Edelgard returned to the Empire in 1174.
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By then, Ionius IX had become little more than a political puppet for Duke Aegir. Powerless, he could only watch in bitter silence as the Adrestian nobles and Those Who Slither in the Dark conducted torturous Crest experiments on his children in an effort to create the perfect ruler for the Empire. Only Edelgard survived the ordeal and bore a second crest as a result, the Crest of Flames.
Ionius IX remained emperor until 1180. After spending much of the year studying at the Garreg Mach Monastery Officers Academy, Edelgard returned to Enbarr to visit her father at the Imperial Palace and demand the crown from him. She may or may not have invited Byleth to accompany her and bear witness to the succession, a role traditionally filled by the archbishop of the Church of Seiros. Feeble and near death, Ionius IX gratefully complied with his daughter's plea to relieve him of the heavy burden of rule and abdicated in a brief ritual. Duke Aegir then arrived in the throne room and was promptly relieved of his duties as prime minister by the newly-crowned Emperor Edelgard von Hresvelg.
Edelgard later revoked Duke Aegir's title and confiscated his lands, restoring the monarchy's strength. The other conspirators of the Insurrection of the Seven were similarly punished for their crimes. Ionius IX presumably passed away between the coronation and 1185.
Ionius is a variant of the ancient greek name Ionis, which has origins in the hebrew Yochanan, meaning "god is gracious". The common name John shares the same etymology, being one of the variants of this hebrew name.
Ionius was the full name of a late Roman Jurist known as Ionius Apollonius.