Many among them also showed that this was their mandate from their Churches and also from the States of their Provinces. This division of judgment and advice constituted a new obstacle to the National Synod. For those who up to this time had been against the convening of the Synod, eagerly grasping this opportunity, worked in every way to the end that the convening of the Synod, although promised, might be prevented. In this gathering the other Professors and Ministers pleaded with Arminius most earnestly that he would reveal to them, his fellow ministers, freely and fraternally what he had against the doctrine expressed in the Confession and the Catechism. They promised that they would be diligent to give him full satisfaction. They promised that he might be reconciled with his colleagues under honorable conditions, and pleaded that they might from now on live peaceably. And they promised that they would say nothing of that which he would reveal outside of this meeting, if reconciliation were achieved. He, on the other hand, said that this was not advisable for him; and he claimed that he was not bound to do this, seeing that this gathering was not called for that purpose. 

During the following summer, when they held the annual Synod of the South Holland Churches at Delft, Uitenbogaard was admonished to give account to Synod of the reasons why, in the giving of advice concerning the manner in which they would hold the National Synod, he had sided with Arminius and had differed with the other Ministers. The intention was that Synod would consider these reasons and pass judgment on this matter. Uitenbogaard answered that he was accountable only to the States, and not to the Synod. Having been requested to state what he had against the doctrine contained in the Confession and the Catechism of these Churches, he answered that it did not appear advisable to him to do this in that gathering, and that he was not prepared to do this. At this Synod inquiry was also made whether, according to the decision of the preceding Synod, any objections or comments concerning the Confession and the Catechism were handed in to the Classis. Then the Delegates of each Classis answered that almost all the Ministers in the Classes had testified that they had no objections against the adopted doctrine, but that those who testified that they had some objections had not been willing to make them known, either because they said that they were not yet ready, or that they did not deem it advisable. On this account, the Synod again decided to order them anew that they, without any excuses, refusal, and postponement, should immediately reveal all the objections which they had against the adopted doctrine, each one in his own Classis.

It also became clear at the Synod that in every way the disagreements in the churches were increasing greatly. It became plain that young men, coming from the Academy of Leiden and the instruction of Arminius, having been called to the ministry of the Churches, when they were examined, hid their views by speaking ambiguously; but, having been admitted to the ministry, they immediately stirred up new disputes, stood for new ideas, and boasted that they had various objections against the adopted doctrine. It became manifest that in the Classes and Consistories bitter disagreements and disputes concerning many points of doctrine arose among the Ministers. It also became clear that among the people themselves, to the great damage and disturbance of the Churches, various wranglings and arguments concerning the doctrine were heard. Yea, the beginnings of schisms were noticed. Further, it came out that the Ministers who were siding with Arminius often secretly held various meetings where they laid plans concerning the advancements of their doctrinal views. And it became plain that the people everywhere were becoming more and more divided. On this account, the Synod, judging that the remedy for this evil might no longer be postponed, and seeing that the hope of gaining a National Synod was very uncertain on account of the divergence of advice and judgments, decided, upon the advice of the Delegates, to request of the States of Holland and West-Friesland that from the two South and North-Holland Synods a Provincial Synod might be authorized at the first opportunity for the quieting and removal of these difficulties (as had been done before in similar difficulties). The Deputies of both Synods showed these daily increasing difficulties thoroughly to the States, and requested the immediate convening of this Provincial Synod for the removal of these difficulties. But although the Delegates, September 14, had given great hope, nevertheless they were not able to obtain a Provincial Synod, due to the fact that there were negotiations under way with the enemy concerning a truce, and the States, being busy on this account with very important matters of the Republic, had not been able to consider these ecclesiastical matters. Meanwhile Arminius, seeing that the Churches persisted in trying to resolve matters through lawful ecclesiastical judgment, wanted to escape this trap; and through requests to the States, April 30, 1608, he managed to get his case treated by the Counselors in the High Council by politicians (in distinction from ecclesiastics, HCH); and on May 14, Gomarus was ordered to appear before them in conference with Arminius in the presence of the Ministers who recently had been in a preparatory gathering from South and North-Holland. The Deputies of the Churches, having understood this, again requested the States of Holland and West-Friesland that the Provincial Synod might be authorized instead of this conference before the High Council, in order that at this Synod they might take cognizance of and pass judgment concerning this ecclesiastical matter. Their reason was that ecclesiastical persons, experienced in these things and lawfully delegated by the churches and empowered to pass judgment, should deal with this matter. The States merely answered that to take cognizance of such matters was enjoined upon the High Council, and that judgment concerning these matters would thereafter be left to the Provincial or National Synod. 

At this conference they first debated at length concerning the order of treatment. Arminius asserted that Gomarus must assume the position of accuser, and that he was only responsible to defend himself. Gomarus, on the contrary, thought that such a procedure was both unfair and improper, especially in an ecclesiastical matter before political Judges. Further, he said that he was indeed ready to show before a lawful Synod that Arminius had proposed doctrines which were in conflict with God’s Word and with the Confession and the Catechism of the Netherlands Churches, but that this could not be done there without pre-judgment of the case. Gomarus believed that this conference, in order to adhere to the purpose of the States, could better be conducted thus, that without mutual accusations each of them should present and express clearly his views concerning every item of doctrine. This would be the best way, according to him, to bring out clearly at this, conference in what points they agreed or disagreed. He stated that as far as he was concerned, he would not refuse to declare his views concerning all matters of doctrine, as much as might be desired of anyone, to the full and forthrightly. But he said that also Arminius, if he wanted to present himself as a faithful Teacher, was obligated to declare his views in the same way and no longer to make use of such alibis. In spite of this, Arminius stuck to his original intention, so that he finally cried out that he was amazed, considering the various rumors of his false teachings flying through all the churches, and considering that they said that the fire kindled by him was now bursting out above the roofs of the Churches—that he was amazed that until now no one had been found who dared to present any accusation against him. In order to counteract this boldness of Arminius, Gomarus took it upon himself to prove that Arminius had taught one of the chief articles of our faith, namely, that of the justification of man before God, in such a way that his doctrine conflicted with God’s Word and with the Confession of the Netherlands Churches. For proof of this he adduced Arminius’ own words from a document written in his own hand, in which he asserted that in man’s justification before God the righteousness of Christ is not reckoned for righteousness, but that faith itself, or the act of faith, through a gracious acceptance, is by God held and accounted for our righteousness whereby we are justified before God. When Arminius saw that he was trapped, and when he saw that because of the clear proof he could not deny this accusation, then he began to consent to a different method of procedure. He proposed that every one should put in writing and sign his opinions concerning the chief items of doctrine about which he believed there was disagreement, should comprehend these views in certain Articles, and that thereafter everyone would signify his objections from the opposite side. This Conference being ended, the Counselors of the High Council gave a report of it to the States; and they said that they judged that, in so far as they had been able to gather from the Conference, the differences between these two Professors were not of such great importance, and that they consisted chiefly of some cunning disputes concerning predestination, which, through the exercise of mutual forbearance, could be overlooked. But Gomarus insisted that the difference in their views was so important that with the views of Arminius he would not dare appear in the judgment of God. Moreover, he warned that unless they would in due time seek to remedy matters, it was to be feared that in a short time the one Province would rise up against the other, the one Church against the other, the one City against the other, and the citizens against one an other. The States wanted the documents signed by both sides in this Conference to be kept in the High Council until the National Synod, and they wanted the contents of these documents imparted to no one. This Conference, however, had not removed the anxieties of the Churches, but rather increased them, the more so because what took place at the Conference was not made known to the Churches. For people, judged, not without reason, that this was done to favor Arminius, in order that his views would not become revealed. The Churches meanwhile did not cease through their Deputies earnestly to petition the States that this ecclesiastical matter, which could not be postponed without great danger to the Churches, might be immediately investigated and disposed of in the gathering of a lawful Provincial or National Synod. When Arminius learned of this, he brought it about through Uitenbogaard, whose influence at that time was great with many Regents of the Fatherland, that the States also ordered even the annual Synods, both of South and North-Holland (the time of which was now approaching) to be postponed. Because this could not be done without extreme damage to the Churches, the Churches made known anew their objections to the states. They requested either that both annual Synods, that of South as well as that of North-Holland, might be held as usual, or that from the two one Provincial Synod might immediately be authorized (as had also been requested previously). In answer to this request, the States, June 28, 1608, declared that they intended to convene a Provincial Synod for this purpose during the following October. When the Churches learned of this, all the Ministers siding with Arminius were again admonished, September 4 and 12, that they should reveal their objections everyone in his own Classis, in order that these might be lawfully brought to the coming Synod. But just as before, so also now everyone refused to do this, with the usual alibis. And when it was almost October and the Churches persisted in the convening of the promised Provincial Synod, it was again postponed for two months; and meanwhile the Churches were allowed to hold the annual particular Synods, both in South and in North-Holland, but with this condition, that the matter of Arminius should not be treated by them, because this was to be reserved for the Provincial Synod.