The contest between Theophilos and John Chrysostom which began at John’s ordination now came to its climax. The Long Brothers and the eighty fellow Nitrian monks with them had arrived in Constantinople in 400 and immediately prostrated themselves before John, recounting all of the horrendous acts performed against them by Theophilos. John took two important steps: he forbade the monks to speak publicly about their trials and he sent a personal letter to Theophilos begging that he receive them back into fellowship.
When Theophilos received the letter from John he realized that the Nitrian monks were in a prime position to have him convicted before the Emperor. Therefore Theophilos sent agents to Constantinople to stir up lies about the Long Brothers. When the Nitrian monks learned of this move they submitted formal charges to John against Theophilos. Upon receiving these charges John sent another letter to Theophilos to inform him of the predicament and that he could not convince the monks to leave the city. Theophilos in turn sent a letter back to John advising him to mind his own business.
I think you are not unaware of the ordinance of the Nicene canons forbidding a bishop to adjudicate a case which falls outside his ecclesiastical area. If however you were unaware, now that you have been informed refrain from meddling with accusation brought against me. If it were necessary for me to be put on trial, it would be before Egyptian judges and not before you, who live more than seventy-five days’ journey away. 
John received this letter from Theophilos in 402 and consequently decided that there was nothing more he could do for the Nitrian monks. This, however, was not a satisfactory reply to the monks who had suffered at the hands of the Alexandrian bishop. They appealed directly to the Empress Eudoxia as she was riding in her carriage. Eudoxia, upon hearing the charges against Theophilos, immediately sent word to Theophilos ordering him to appear before a synod of bishops in Constantinople presided over by John. At this point Theophilos began to plan a way to undermine John, have him deposed, and save his own skin in the process. His first move, although not entirely political, was to send Epiphanios to urge John to convene a council against Origenism. However, upon arriving in Constantinople Epiphanios refused to meet with John. Apparently Theophilos had convinced Epiphanios that John harbored the Long Brothers because John himself was an Origenist. This accusation would not have been difficult to prove due to John’s acquaintances. His “lady” Olympias (John’s best friend) was an acquaintance of Melinia and Rufinus who had been instrumental in the conversion of Evagrios Pontikos to the monastic life. Palladias, one of John’s most avid supporters, was also a long-time friend of Melania and John Cassian (known for his sympathies toward Evagrios). John had even appointed a student of Evagrios (Herakleides) to bishop of Ephesos. The attempt of Epiphanios to have John and the bishops in the city sign an anti-Origenist document failed. After attempting to disrupt the services of the Great Church his life was threatened, and having opportunity to hear the story of the Nitrian monks he was convinced of their orthodoxy. Theophilos’ plan had failed.
After more than a year of traveling by land (a route which enabled him to turn every bishop along the way against John) Theophilos finally entered Constantinople in August 403. Theophilos spent the next three weeks interviewing every person in the city (and persons from those cities through which he passed on his journey) who had condemning evidence against John. This was not a difficult task for John had gained many enemies due to his swift and rough reform methods. Even the Empress Eudoxia had been offended on numerous occasions by John’s often direct attacks on her vanity. In May 403, shortly before Epiphanios’ departure, John preached a sermon against the weaknesses of women. The congregation thought that he was referring to Eudoxia. The news of this sermon infuriated the Empress who besought Arkadios to have John punished. Arkadios, however, followed the suggestions of his political advisors and sent word to John to convene the trial to consider the guilt of Theophilos. John refused to follow Arkadios’ orders to act as the judge against Theophilos. John believed that if he were to act as judge over the bishop of another see he would be breaking the canons of the church, thus condemning himself before a higher judge. Arkadios, already pressured by Eudoxia, pronounced in his anger against John’s decision that Theophilos would be the new judge and that the trial would no longer be between the Nitrian monks and the Alexandrian bishop but between John and the Eastern Empire.
 Kelley, 197.  Ibid., 197, 198.