It seems to be Natural Evolution Enemies (fixed). Deactivating it removes the frame drops. I'm now using the Redux Version of the Mod which doesn't have this problem.

The best way to get people to help you find the source of lag spikes is by showing the ingame timing information. It shows which things, and which mods, take's the most time, and will show you which mod is the culprit.

If you don't know how, press F4, scroll down to `show-timing-information` or ...

Hello there,

After playing for nearly 11 hours on my save the game suddenly decided to start lagging (3 seconds normal FPS, 3 seconds lag, repeat)
I think it's a mod problem as I deconstructed my entire factory and killed every enemy using commands and it still lagged. Only a new game fixed it but ...