Startup fails but (most) files still are accessible

SmartSpot

TS Rookie
I was cleaning out my computer case. The next time I turned it on Windows gave me the error message that "A required device isn’t connected or cannot be accessed" with error code 0xc000000e. I rechecked the cables to the SSD and disconnected all non-essentials. I restarted the computer and got to "your PC did not start correctly" where I could get to the command prompt.

I tried running
bootrec /rebuildbcd
but it couldn't find any windows installations. Also the C:\Windows folder is missing. I wasn't able to get it to start in safe mode. However, through the command prompt, it seems all my files are there and I can open the text ones.

What can I do next?