Extraterrestrial particles and the atmosphere
When extraterrestrial charged particles precipitate into the middle atmosphere of Earth (lower than 100 km), they ionize the most abundant species: O2, N2, and H2O. This starts a chain of very fast ionic reactions in a region that is generally neutral. This reactions are described in detail i.e. on the SIC homepage; however, the outcome of all the ionic reactions in the mesosphere and stratosphere is that N2 is transferred into N or NO, and H2O is transferred into H and OH. N, NO, H and OH are much more reactive than N2 and H2O, so ionisation of the middle atmosphere due to particle precipitation events makes the mesosphere and stratosphere more reactive.
NOx, HOx, and ozone
Odd nitrogen NOx (N and NO) and odd hydrogen HOx (H and OH) both destroy ozone in katalytic cycles like these:
H + O3 -> OH + O2
OH + O -> H + O2
NO + O3 -> NO2 + O2
NO2 + O -> NO + O2
Ozone is destroyed in every cycle, while the reactands (H respectively NO) are reformed in the second step; so, ozone is destroyed very effectively, while the NOx or HOx concentrations are not affected. Generally, HOx is more effective for ozone destruction above ca. 40 km altitude, NOx below ca. 40 km altitude.
To summarise: Precipitation of charged particles produces NOx and HOx, which both destroy ozone in katalytic cycles. HOx is very short-lived in the middle atmosphere, and enhanced values of HOx only persist as long as a particle-events lasts; NOx, on the other hand, is more long-lived, and enhanced values can persist for weeks or even months after particle events. NOx lives even long enough that it can be transported down into the region of the ozone layer (20-30 km), where enhanced values of NOx can affect the total amount of ozone in the atmosphere significantly. This in turn may have consequences for live on earth, as the ozone layer shields the lower atmosphere - and the biosphere - from the solar UV radiation.
Charged particles and the magnetic field
Where and how far extraterrestrial charged particles precipitate into the atmosphere is determined by the strengths and form of the Earth's geomagnetic field: charged particles moving through the solar system along the field lines of the solar magnetic field can precipitate into the Earth's atmosphere only in the polar cap regions, around the magnetic poles (at magnetic latitudes > 60 degree). Without a magnetic field, charged particle precipitation would be possible even into regions which are at the moment shielded by the magnetic field.