With your pool draining, washing with bleach and refilling is probably easiest.
You need to TEST your water daily for adequate chlorine levels and proper pH balance. You'll need a proper test kit and the one in Pooldoc's sig, the Taylor K-2006 is the one.
Without knowing your stabilizer level and chlorine levels anything can happen and did. If there are living worms, GUARANTEED your chlorine level is too low!
I'd replace the filter cartridge too with the new water. You usually cannot run MORE than two weeks with an Intex cart without cleaning it.