So I kinda figure it's either the PSU or one of my hard drives, but what the issue is is that me PC first makes a click sound (as if I physically shut it down), then restarts some time after.
When it restarts it makes a bit noisier click sound, same as the power button switching does.
I have verified it's not ghosts or little green men.
I can't say for certain about Martians.
It's just weird. I'll be unplugging both HDD's today to see if it goes away.
Then one-by-one plug things in/out.
It's most likely originating from a relay switching inside your PSU. It's perfectly normal - my Be Quiet unit (slightly ironic, I know) does it and I've never had any issues.
If it's the same contactor sound your PC makes when booting up and shutting down, it's most likely your PSU. What is the model of your PSU? How old is it?
Due to heat, materials can bend. If a material was under alot of tension already before, it can sometimes pop (click sound) to release it. Just like poping a pimple.
Depends on what exactly it is and how exactly it is poping it might be a problem but usually you should be fine.