Bike tyre damage from riding on a flat?
Completely remove the tire, tube. Check the rim tape is sitting correctly, and remove that. Clean the rim of any debris that might have go inside it and under the rim tape.
With three punctures in the inside take a very close look at the rim tape for any sign of damage. Also check the rim for sharp burrs than may have occurred due to riding on the flat.  If the rim tape is looking good, clean it and reinstall. If in doubt, get a new one.
Its possible that the tube suffered a lot of damage from riding flat, I would put in a new tube, if that punctures, I would then replace the rim tape and tire (and maybe another tube).
Your tolerance for spending money and putting up with ongoing punctures determines when to buy new items. I really dislike punctures, so would be replacing rim tape, tire and tube immediately.