Historical Context
Theophilus served as Archbishop of Alexandria from 385 to 412 and was succeeded by his nephew Cyril of Alexandria. Early in his tenure he had supported the teachings of Origen and kept good relations with Origen's monastic followers, including the four monks of Scetis known as the Tall Brothers. Relations soured around 395 over a quarrel with the archpriest Isidore, a friend of the Scetic monks.
By 399 Theophilus had turned against Isidore with both slanders and violence, and when Isidore sought protection among the Nitrian monks, the patriarch turned against the monks as well and against Origen's teachings. At a synod held in Alexandria — dated to 400 or 401 in the sources — Origenism was condemned. Theophilus then attacked the settlements of Nitria, burned their buildings, and dealt harshly with the monks he captured. The Scetic monks fled to Palestine, while the Tall Brothers went on to Constantinople to seek protection from the Emperor Arcadius and Archbishop John Chrysostom.
The conflict formed part of what is known as the First Origenist Crisis, which began in Palestine in the late fourth century and spread to Egypt by 399. General historical summaries of the crisis describe expulsion, exile, and the destruction of monastic settlements rather than a numbered massacre; the figure of ten thousand and the explicitly martyric framing belong to the synaxarion and liturgical tradition. The wider quarrel continued to reverberate, culminating in Theophilus's role in the deposition of John Chrysostom at the Council of the Oak in 403.