The thermosphere is the uppermost layer of our atmosphere. It is driven from below by tides and gravity waves, from within by absorption of solar EUV, and from above by the magnetosphere and solar wind. It is important to understand the behaviour of the system because the thermosphere is also home to a wide variety of orbiting satellites, the International Space Station, and 20,000+ pieces of orbital debris. In this talk, I will describe how collision avoidance is dependent on knowing what the thermosphere is going to do (which is hard!), and how the thermosphere reacts to energy input from the magnetosphere in the form of substorms. These auroral energy input events have different stages (growth, onset, recovery), which each effect the thermosphere in different ways. This talk will describe aspects of predicting satellite collisions and the modelling of thermospheric reaction to the different stages of substorms.