This is a weird problem, I have raspibian OS Jessie installed on my pi3 . So the problem is Raspberry pi boots to root user in terminal when mounted USB HDD is not plugged into USB port.
I have set up manual mount from /etc/fstab ( follow this link how and why I mount up manually https://raspberrypi.stackexchange.com/a/53622/49991)
To me it feels like it's a bug that if external USB drive is not mounted it falls back to root user in terminal mode. Well that shouldn't happen at all.
proc /proc proc defaults 0 0
/dev/mmcblk0p1 /boot vfat defaults 0 2
/dev/mmcblk0p2 / ext4 defaults,noatime 0 1
# a swapfile is not a swap partition, no line here
# use dphys-swapfile swap[on|off] for that
# New NTFS HD: Archives&Backup on Sat Aug 20- 13:00:00 IST 2016
# UUID=120063E80063D171 /home/pi/USBHDD/ ntfs rw,auto,users,uid=pi,gid=pi 0 0 /dev/sda1 /home/pi/USBHDD/ auto,users,rw$
the last line above is where I have commented both ways to mount the disk, Earlier I was using UUID method but later I decided to use the one that starts with /dev/sda1 but since HDD is not with me I had to disable it.
