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Any impact powerful to significantly alter the orbit of a planet is also going to be powerful enough to vaporise the entire surface of the planet anyway - however 40k has never been big on actual science anyway

Other options include:

- The Ecological collapse

Could simply be a natural phenomenon, or it can be caused by a bio-virus introduced at the bottom of the food chain - imagine killing all algae on Earth...

- The Nuclear Winter

This can also be caused by similar events such as a super-volcano or significant asteroid impacts

- Something goes wrong with the star

This is a fun one! Firstly you have the possiblity of a Helium flash event taking place - basically it sears the side of the planet's surface facing the star, and wrecks the overall atmosphere, while still leaving the possibility of life surviving on the other side.

Alternatively you could simply have the star move to a different point in the main sequence with subsequent effects on the biosphere.

Both of these would work very well with the Necrons - they could be using the star as a source of energy, causing these alterations but not caring what happens to the solar system.

- The massive radiation burst

Another fun one - a nearby stellar event irradiates half of the planet's surface, and destroy's the ozone layer. Could also be caused by a nearby Soft Gamma Repeater, Nova or Supernova

- For some other options take a look here...