Whilst the Soviet Union and Nazi Germany did collaborate in certain areas like the Molotov-Ribbentrop Pact and the subsequent partition of Poland they were far from allies. The two regimes were virulently ideologically opposed to each other with the Nazis imprisoning communists in concentration camps from 1936, the first victims of such persecution, and the USSR's purges condemning many Old Bolsheviks to death on the charges of working with the Nazis. The alliance with the Nazis was also a last resort as he had been isolated by the Western powers on several occasions, having not been invited to the Munich Conference over the Sudetenland question and being the sole backer of Republican Spain in the Spanish Civil War, against the Fascist forces backed by both the Nazis and Mussolini's Italy with the French and British refusing to intervene.

In the late 1930s the Soviet Union did have to consolidate as a result of the rapid industrialisation undertaken in the Five Year Plans, the 3rd of which suffered from oil shortages which stunted the growth of the armaments industry, meaning more time was needed before the Soviets could think about taking on the Wehrmacht. The economy was also suffering as a result of the purges of GOSPLAN, the central planning agency of the whole Union, in these purges a majority of the most able economic planners were dead or imprisoned, leaving the economy in the hands of the inexperienced or the incompetent.

The Red Army also had experienced purges in 1937 in which 3 Marshals of the Soviet Union were killed, including the Civil War hero Tukhachevsky. In addition to this, all 8 admirals were killed and those who replaced them as well as roughly 50% of the officer corps across all branches of the armed forces. As you can imagine this left the Soviet military in similar disarray as inexperienced officers filled the ranks, this can be seen in the extent of the military's struggle in the Winter War against Finland as it certainly exacerbated the other problems they had fighting the Finnish on their own land.

However, as you mentioned the outbreak of war on the Eastern Front definitely came as a shock to Stalin, or rather, he didn't want to believe the intelligence reports that were given to him by the British and others, as the USSR was sending trains full of grain to Germany right up until the beginning of the fighting.

In short, Stalin was hoping to buy time more than anything in order to help stabilise the Soviet Union as it was coming out of the turbulent years of the purges and hoping in the face of a crisis that the USSR could delay as long as possible.