Quality factor is a primary cost driver for high energy, continuous wave (CW) SRF linacs like the LCLS-II X-ray free electron laser currently under construction. Taking this into account, several innovations were introduced in the LCLS-II cryomodule design to push substantially beyond the previous state-of-the-art quality factor achieved in operation. This includes the first ever implementation of the nitrogen doping cavity treatment, the capability to provide high mass flow cooldown to improve expulsion of magnetic flux based on recent R&D, high performance magnetic shielding, and other critical subcomponents. To evaluate the implementation of these new cryomodule features, two prototype cryomodules were produced. In this paper, we present results from the prototype cryomodule assembled at Fermilab, which achieved unprecedented cavity quality factors of 3.0e10 at a nominal cryomodule voltage. We overview cavity performance, procedures to achieve ambient magnetic field < 5 mG at the cavity wall, and the successful demonstration of high mass flow cooldown in a cryomodule. The cavity performance under various cool down conditions are presented as well to show the impact of flux expulsion on Q0.