Towards the end of the ninth century, due to the collapse of the Holy Roman Empire the Catholic Church had to rely upon powerful European nobles for support. Pope Stephen V approached Arnulf of Carinthia to protect Rome from "pagan and evil Christians". After he refused, Stephen V had to rely upon Guy III of Spoleto instead. Guy agreed to protect Rome as long as he was named as the Holy Roman Emperor, to which Stephen V acceded. After Stephen V's death, Pope Formosus was elected. Formosus and Guy were reluctant allies, and Guy forced Formosus to crown him emperor again and to name his son, Lambert, as co-emperor and successor. Formosus did so, but after Guy's death, he lobbied Arnulf to rescue Rome from the Spoletans. Arnulf agreed, and Formosus subsequently appointed him as the Holy Roman Emperor in 894. Both Arnulf and Formosus died within a few years of the coronation, and the new pope, Stephen VI, crowned Lambert as the new emperor shortly thereafter.
In January 897, Stephen VI held what is known as the "Cadaver Synod". He had the body of Formosus exhumed from St. Peter's Basilica and dressed in pontifical vestments. The dead pope was charged with "perjury, violating the canons prohibiting the translation of bishops, and coveting the papacy." Formosus' defence was provided by a deacon, but he was found guilty of all the charges. The synod annulled all of Formosus' acts and ordinations. Formosus' body was reburied in a common grave, and then thrown in the river Tiber. Supporters of Formosus rebelled, and seven months after the synod, Stephen VI was deposed, and died soon after in prison. His replacement, Pope Romanus is generally assumed to have been pro-Formosus, but he was only pope for four months before he was deposed and made a monk.
Little is known of Theodore's background; he is recorded as being born a Roman, and the son of Photios I of Constantinople, who was the Patriarch of Constantinople. His brother Theodosius (or Theosius) was also a bishop. He was ordained as a priest by Stephen V. The exact dates of his papal reign are unknown, but modern sources generally agree that he was pope for twenty days during December 897. Flodoard, a tenth-century French chronicler, only credited Theodore with a twelve-day reign, while in his history of the popes, Alexis-François Artaud de Montor listed Theodore's reign as being twenty days, from 12 February to 3 March 898.
Like his predecessor, Theodore was a supporter of Formosus. Some historians believe that Romanus had been deposed because he had not acted to restore Formosus' honour quickly enough, though others suggest that he was removed by supporters of Stephen VI. In either case, Theodore immediately threw himself into the task of undoing the "Cadaver Synod". He called his own synod, which annulled the rulings set out by Stephen VI. In so doing, he restored the acts and ordinations of Pope Formosus, including the restoration of a large number of clergy and bishops to their offices. Theodore also ordered Formosus' body to be recovered from the harbour of Portus, where it had been secretly buried, and restored to the original grave at St. Peter's Basilica. Like Romanus before him, Theodore bestowed a privilege upon the See of Grado, and had a coin minted, bearing the name of Lambert on the obverse, and "Scs. Petrus" and "Thedr." on the reverse.
Flodoard cast Theodore in a positive light, describing him as "beloved of the clergy, a friend of peace, temperate, chaste, affable and a great lover of the poor." He died in office, though the cause of his death is unknown. Because of this, some writers, such as, Wendy Reardon) suggest the possibility of foul play. Horace Kinder Mann offers a different suggestion in his papal history, noting that it is possible that Popes who were "infirm or even older than [...] their predecessors" might have been elected intentionally. Theodore was buried at St. Peter's Basilica, but his tomb was destroyed during the demolition of the old basilica in the seventeenth century.
After Theodore's death, both Pope John IX and Sergius III claimed to have been elected pope; the latter was excommunicated and driven from the city, though he did later become pope in 904. John IX held synods reaffirming that of Theodore II, and he further banned the trial of people after their death. In turn, Sergius III later annulled the synods of Theodore II and John IX, and reinstated the validity of the "Cadaver Synod".