Energetic particle precipitation during solar active periods induces enhancements of NOx (N, NO, NO2) in the lower thermosphere/mesosphere which can be transported to the stratosphere within the polar vortex. The quantitative contribution of these NOx intrusions to ozone chemistry in the stratosphere is still under discussion. Here we present simulations with a three-dimensional model of the middle atmosphere where NOx enhancements in the lower mesosphere have been taken from the observations of the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) instrument on the European Space Agency satellite ENVISAT. Covering the period from July 2002 to March 2004 these observations include the strong solar proton event in fall 2003 and intrusions connected to auroral events during the Arctic and Antarctic winters. The comparison of the disturbed run with the undisturbed model run allows a quantitative assessment of the long-term influence of NOx intrusions on stratospheric chemistry in general and the ozone concentration in particular. From the model simulation, we estimate for the period from July 2002 to March 2004 that in total, an additional 5.4 Gigamol NOy has been brought into the middle atmosphere. This represents in early 2004 about 5% of the global NOy mass in the middle atmosphere. A 2 year decay time for such enhancements is estimated from the model. Persistent reduction of ozone concentration in the stratosphere caused by the NOx intrusions can be followed in the simulation for several months. This reduction is restricted to high latitudes and amounts to several Dobson units in the total ozone column.