Just to post an update, I've been digging into this issue for quite some time now and I think I was able to fix it. I will post it here in case anyone is able to use this information.
Firstly, make a backup of your registry just in case.
After rebooting and relaunching explorer.exe, I dug through a bunch of forums and help guides. The main takeaway is that something changed my registry so that explorer.exe would not run on startup. After backing up my registry through regedit, I started poking around and comparing my registry to my friends'. There were two main registries I focused on, due to being mentioned in other people's issues. Its the AutoRun key under the Command Processor folder and the Shell key under the Winlogon folder.
The trick is, these keys and folders are located in two paths each: under the CURRENT_USER and under the LOCAL_MACHINE.
Computer\HKEY_CURRENT_USER\Software\Microsoft\Windows NT\CurrentVersion\Winlogon
Computer\HKEY_CURRENT_USER\Software\Microsoft\Command Processor
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Command Processor
After locating these folders, I first changed the value of the "Shell" keys to " explorer.exe " and then changed the value of any Autorun key to be empty (as in delete the value, not the key itself).
After doing that for all four keys, I rebooted my PC and everything seems to be working OK now. I've checked my PC several times with different scanning stuff and nothing seems to be out of the ordinary. I might one day do a fresh install of Windows 10, but for now I'll leave things as-is and keep my stuff backed up.