If it was me, I would from the USB. Open up a terminal. Sudo or su to root.
run fdisk -l to see which disk is which.
Most likely the disk you boot from will be /dev/sda ( your USB stick )
And your computer disk will be /dev/sdb
But fdisk -l will show you the sizes, so it will easy to tell. ( 32GB vs 512GB or something similar )
I don't know what your partitions look like, but /biosboot or /boot/efi will be a separate partition from /
I would try to run fsck on these. i.e fsck -y /dev/sdb1 fsck -y /dev/sdb2 ( change the device to
whatever yours might be ) Hopefully this will fix it.
One way to tell if the file systems are good. Is you can mount them from your USB drive.
i.e. mount /dev/sdb1 /mnt
If it mounts, the filesystem is probably OK. If it turns out it is a config file.. maybe /etc/fstab
or something like that, at least you can mount the partitions and look through your files. At the very least
you can copy anything important off somewhere else.