From the sounds of it, you've managed to cause a glitch in the game. If you're entered the body while the "tongue" was still present, you bypassed a few critical events in the game. The remainder of this post contains spoilers so fair warning.
Li is originally found in the Veil (he's the oddly dressed diver who you can follow into a cave)
You'll need him to access the sunken city as he has the key to the lock.
Once you beat the sunken city, the "tongue" retracts in the body.
As a means to correct your glitch, you have 2 options.
The first is, unfortunately, starting over.
The second is by contacting Alec and explaining the situation. I've seen others make the same mistake/glitch you did and he was able to edit their save file, putting you, once again, in the proper condition to finish the storyline.
