Molecular clouds are thought to be made from overdensities, or filamentary structures, in the interstellar medium where lots of atomic hydrogen is collected. We don't know precisely how these filamentary structures themselves are created, but the leading theory includes contributions from:

1. Spiral density waves (the same waves that form galactic spiral arms) and other global galactic gravitational instabilities

2. "Supershells", basically the compression of the ISM by stellar winds, supernovae, and other ionizing radiation.

3. Turbulent compression, the stochastic movement of the ISM

We don't know the relative importance of each of these processes, but that's the general idea.

[Big ol' review of Star Formation for the brave of heart] (https://arxiv.org/abs/0707.3514)