What causes the Aurora? Why does it look like it does?
During a solar storm, or from a solar flare, ionized protons and electrons are emitted as from the sun as plasma (containing magnetic fields from the sun) and fly out into the solar system. Sometimes these the plasma is directed towards earth and arrive at our magnetic fields at supersonic speeds.
The interaction of the plasma and the earth’s magnetic field causes the aurora.
The best description of this process is here: Department of Physics, University of Oslo
Oxygen when returning to its ground state gives off a green photon in 3/4ths of a second, while the red photon takes much longer (~2 minutes). If the oxygen atom collides with another atom during that 2 mintues, the red photon is not emitted. So, at higher altitudes, where the atmosphere is less dense, and the oxygen atom has less chance of colliding with other atoms, the red auroras are seen.
A great FAQ page about Auroras.