Remaining formally within the Tcheka, Aralov, from the first day of his work in military intelligence, had to become a rival and consequently enemy of the Tchekists. This had entered into Lenin's calculations; he had not been slow to see that it would be impossible for Aralov to avoid daily skirmishes with the Tchekists on the most mundane questions, and that this would inevitably lead to a confrontation which would preclude any possibility of Aralov being exploited as a trusted Tchekist. But this was not all. In the case of any agreement with the Army, not one of the Army's chiefs would dare to trust Aralov. The GRU would be a part of the Army but the Army would not be able to make use of the GRU in the struggle against the Party and the Tcheka.

Lenin's calculations proved themselves sound remarkably quickly. In the spring of 1919 the reinforced army under Trotsky's leadership openly came out against the Party's meddling in the affairs of the Army. A united group of Army delegates, the so-called 'Military Opposition', at the eighth congress of the Party in March 1919, demanded de facto independence of the Army from Party influences. At that time it was still permitted to express personal opinions at party conferences, and more than 100 delegates out of 269 declared themselves in favour of the military programme. There were widespread abstentions and the Party and the Tcheka found themselves in a minority at their own conference.

Only a few votes were necessary to secure the complete and legal victory of the Army, but at this point the delegates from the military intelligence service, knowing the heavy hand of Aralov, maintained an icy silence and strict neutrality. Then at the most dramatic moment of the session Aralov spoke critically of the military opposition, after which the delegates of the military intelligence service with one voice supported the Party. The number of supporters of the military opposition shrank to ninety-five, a clear defeat.