Shawn injured his back Jan 98 when he took a bump over the ropes and his back smacked the end of the casket crushing 2 discs in his back.
Because of the adrenaline he didn't know how bad it was until the next morning he couldn't physically get out of bed.
So he didn't wrestle for nearly 2 months until WM 14 where he would drop the title to Austin and then go get back surgery. (If you watch this match you can see the agony and pain Shawn was in)
He didn't wrestle again until late 2002 when he made his comeback.
At the time I believed it was a legit career ending injury however after listening to Jim Cornettes podcast I've come to the conclusion that Jim is probably right. He said Michaels messed up his back and then got surgery. Vince was still paying Shawn up until 2001 because WCW was still in business and he didn't ever want Shawn to leave. When Shawn's contract ended in 2001, WCW was also bought out by Vince.
In 2002 Shawn made his comeback.
So my guess is Shawn's back was really injured bad but he chose to collect his paychecks at home because he was going to get paid the same whether he wrestled or not.
This led to a severe pill addiction and then he found Jesus and turned his life around.
Also from 98 to 01 Shawn was the commissioner of the WWF, special guest referee several times and then he would just make random appearances probably because he was obligated to.
He would do sweet chin music here and there but never ever wrestle until 2002.