Here's a little Breakdown!

Adding atmosphere using Nuke particles for the rain and fog
Different AOVs from Arnold allow changing the landscape lighting to make the lightnings.
The cloud DMP has two different states, the normal one and one backlit by lightning.

To be able to make the thunderstorm feel 'alive' I animated the clouds using a little tool I made for that purpose, by painting a vector direction it is possible to animate that over time and loop it automatically. The speed and how fast it loops can then be controlled using linked expressions.
This has helped a lot to make the static image feel volumetric
Additionally I projected the clouds on a plane with added displacement to add natural feeling volume to the 2D sky
Below is a little RnD from the beginning of the project:
Heres what the cloud flow tool looks like on a stylised image:
We decided to texture the environment fully in comp, this enabled us to go for a more stylised look, do iterations way faster and be able to paint multiple assets simultaneously while always seeing the big picture and the composition.

By rendering out a Basecolour pass, I was able to seperate lighting from colour by division, then I could paint underneath the lighting, and multiply the lighting back over later.

Additionally using the normal-pass I added an edge detect to add more texture that followed what was already there in mesh

Here are some befores and afters:

And some very early tests of this technique.
top left the painted basecolour, bottom right the original render
Here is some concept art I painted at the very beginning of the project when we were still figuring out the overall direction:

And here the lighting process in pictures starting with the first render:
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