The rebels were quickly ready for action; and in the year 1394, as Wenceslaus was on his way to Prague, he was seized by Jodok and his followers, and imprisoned in the Castle of Prague. The demands of the insurgent nobles were now formulated. They insisted that Wenceslaus should leave them in possession of all the fortresses that had been pledged to them, and that he should appoint Jodok as his Viceroy in Bohemia. Duke John of Görlitz, the youngest brother of Wenceslaus, hastened to the rescue of the king; and, though Jodok succeeded in carrying off his prisoner to Austria, John was welcomed by the citizens of Prague, who swore to recognise him as the administrator of the country till the King should once more be at liberty to act.

In the meantime the princes of the Empire had become indignant at the treatment of their Emperor; and they persuaded the Duke of Austria to set him free. Wenceslaus returned, embittered and suspicious, to his kingdom; and his brother John soon found that the position of liberator and peacemaker was a very difficult one. The rebel nobles had fled to Austria, whence they made raids upon their native country; John attempted to make peace between the king and the insurgents; but, when Wenceslaus found that John had mistaken the extent of the powers entrusted to him by the rebels, he accused his brother of deceiving him, and deprived him of his vice-royalty. Many of the citizens of Prague had become attached to John, and they remonstrated against his deposition. Thereupon Wenceslaus deposed all the members of the Town Council, appointed a new Council in their place, and then went through the town, accompanied by an executioner, who cut off the heads of the King’s leading opponents at the doors of their houses. In his discontent with John, Wenceslaus now appealed to his brother Sigismund. Sigismund came, and John soon after died, not without suspicion of poison. Sigismund at once persuaded Wenceslaus to recognise him as his heir if he should die without sons, to appoint a Council of the nobles, and to promise not to introduce any changes in the government without the consent of that Council.

The hollowness of the peace which followed was very quickly seen. When Jodok came to see the king at Carlstein in the same year, Wenceslaus was so carried away by the recollection of his cousin’s insults, that he had him arrested and imprisoned. Then, suddenly remembering the treaty of peace, he set him free again. But Jodok thought more of his imprisonment than of his liberation; and, though nominally reconciled, the King and the Margrave remained enemies throughout life.

The Bohemian quarrels had, in the meantime, given opportunity for the intrigues of Wenceslaus’s rivals in the Empire. That jealousy which the Electors always felt of the concentration of the Imperial power in any one family, had been for some time directed against the House of Luxemburg. Charles’s extension of Bohemian territory, by the addition of German lands, had caused much suspicion and dislike. But his combination of vigour and self-restraint, and his complete hold over his Bohemian subjects, had prevented the intriguers from making any head during his lifetime. Now, however, the quarrels of Wenceslaus with his subjects had given a double opportunity to his German opponents; for while, on the one hand, they could point to his long detention in Bohemia as a proof of his indifference to Imperial affairs, on the other hand, the disaffection of his Bohemian subjects supplied a hopeful weapon for undermining his power.

His two leading enemies were Rupert, Count Palatine of the Rhine, who aimed at the Imperial dignity, and the Archbishop of Mainz, who had secured his see by a promise to support the intrigues of Rupert. These conspirators succeeded in winning to their side Pope Boniface IX. This Pope had indeed been at first friendly to Wenceslaus; but he had been offended by the readiness with which the King of Bohemia had listened to the French proposals for the election of a new Pope in place of the two rival claimants to the Holy See. Under various pretexts, the Duke of Saxony and the Archbishops of Trier and Köln were drawn into the conspiracy; and so, in February, 1400, the Electors met at Frankfort and resolved to choose a new Emperor.

The most plausible grounds for this deposition were mainly of a negative kind. Wenceslaus was charged with failing to procure a peaceful settlement of the affairs of the Church, and with paying no heed to those wars which were disturbing the Empire. Though Wenceslaus might have found ample excuse for these failures, he could not directly deny them; but the other charges were either false or grossly exaggerated. One of them, however, must be quoted, since it has so much bearing on the troubles which were approaching in the Bohemian kingdom. This was a charge that he “had drowned, burnt, and otherwise murdered and tortured reverend prelates and priests.” This accusation shows that the murder of Nepomuc was to be represented, at the pleasure of Wenceslaus’s enemies, either as part of a general massacre of priests, or as the cruel execution of one specially righteous man.

It was, therefore, as the champion of Holy Church against its oppressor, that Rupert was chosen Holy Roman Emperor. In this character he at once marched into Bohemia and won the support of Jodok and the discontented nobles. Again Wenceslaus was forced to make terms with his enemies; and again Sigismund was called in and appointed Viceroy. But Sigismund gained favour with no party. Jodok and his friends resented the power entrusted to him; the citizens of Bohemia complained of the heavy taxes which he laid upon them; and Wenceslaus resisted his proposal that he should counteract the schemes of Rupert by accompanying Sigismund to Rome, and by accepting the Imperial crown from the Pope. Finding his plans thwarted, Sigismund suddenly seized upon his brother, and carried him off as prisoner to Vienna. From this imprisonment Wenceslaus succeeded in escaping in 1403; and, on his return to Prague, he was welcomed as the liberator of Bohemia from Sigismund.

In the meantime the reform movement had been approaching a crisis. The teacher who, after the death of Milic, had gained most influence in the country, was a Bohemian nobleman named Matthias of Janov. He had not devoted himself so exclusively as Conrad and Milic had done to the denunciation of moral abuses, but had also attacked practices like the worship of images and saints; and he had been the first to bring before the public the question which was afterwards to be so interesting to Bohemians, the granting of the cup to the laity in the Holy Communion. But though this latter fact gives Matthias a kind of historic interest, he seems to have been in the main a source of weakness to the cause which he defended. Never wholly disinterested in his objects, he soon flinched from the attacks of the rulers of the Church; and in 1389 he formally recanted his reforming doctrines.