While driving started running rough SES light came on, now it will not start

Driving home car was just fine running good. All of a sudden started running very rough, SES light came on and started flashing. Pulled over and parked turning engine off. Waited a few minutes and restarted, SES light no longer on but vehicle running very rough and would barely move forward. Turned off again, called tow truck. Checked with scanner and showed no codes. Now it will only crank for a few seconds and end with a loud clunking sound and battery will drain. Have tried to start three times with same result. Have to recharge battery in between tries. Thanks for any help.
OK here is a little update. While trying to figure out what is wrong I cranked engine but it would only crank for a couple of seconds before fully charged battery went dead. I smelled something burning and fan traveled in one direction and as battery went dead the fan started to rotate in the opposite direction! This only took 4 or 5 seconds.