When the solar wind is strong enough, the top part of the aurora appears. It is often red: https://commons.wikimedia.org/w/index.php?title=File%3AAurora_Australis.ogv.
The aurora is the product of the following steps:
- A charged particle from solar wind follows one of Earth's magnetic field lines downwards and polewards.
- The charged particle collides with a atmospheric particle. An electron in the atmospheric particle is excited to a higher energy level.
- After some delay, the electron relaxes to a lower energy level, either a) by emitting light, or b) during a collision with another atmospheric particle.
The two most common aurora colours, green and red are emitted by atomic [non-molecular] oxygen (wavelengths 558 and 630 nm, respectively). Importantly, the decay which emits green light occurs more rapidly than the red one.
At medium altitudes, atomic oxygen is quite abundant. Atom-atom collisions (step 3b) are quite common, so the slow emission of red light is suppressed. The aurora appears green.
At higher altitudes, atomic oxygen is rare. Atom-atom collisions are rare, so red light can also be emitted. This is the standard explanation for why the top of the aurora is red.
However, this explanation does not seem complete. There is no reason why green light should not be emitted at high altitudes (in addition to red light). So why is the top of the aurora red (with no trace of green)?