The mode locking dynamics of a diode-pumped thin-disk laser oscillator with an active multipass cell operated in ambient atmosphere was studied numerically. The numerical results are compared to experimental results of a passively mode-locked thin-disk Yb:YAG laser with several megahertz repetition rate, sub-picosecond pulse duration, and $>10\mu \text{J}$ pulse energy. The numerical simulations prove that the soliton area theorem predicts a correct pulse duration when considering an average pulse energy inside the oscillator. Furthermore, they show a variation in the full width at half-maximum pulse length for the pulse that propagates within the oscillator. This oscillation shows a behavior that is contrary to a change in the pulse length given by the soliton area theorem when considering the real pulse energies at respective points in the resonator. The “breathing” is caused by the strong influence of the self-phase modulation of the ambient atmosphere and large amounts of dispersion resulting in a deviation from the ${\text{sech}}^2$ pulse shape and a chirped pulse.