We present the analysis of 9.7 years Fermi-LAT data of the middle-aged supernova remnant (SNR) W44 and the massive molecular gas complex that surrounds it. The derived spectral energy distribution of the SNR, derived over three decades is improved, with respect to previous observations, both at low ($<$ 100 MeV) and at higher energies ($>$ 100 GeV) allowing us to strongly constrain the hadronic origin of the emission. We also unveil the presence of two extended $\gamma$-ray structures located at two opposite edges of the remnant along its major axis. These two sources do not coincide with any peak in the gas distribution, therefore are interpreted as “CR clouds”, namely as regions of enhanced CR density, consisting of particles that escaped collectively from the remnant along the magnetic field.