At the end of the second to last season I believe Clayton was on some ship and there was some accident and several people apparently were killed. Mac had been trying to find Webb and Sturges (what was his full name?) accidently saw some files of those listed among the dead. Webb's picture was one of them. I don't recall the rest exactly, but Webb was being chased by someone who was trying to kill him. So he faked his death.

I was watching on and off until the last season when I quit at the beginning of it. Harm/Mac was the least of my issues with the show. Personally I thought Mac was crazy to want to be with Harm.

Actually I never expected anything less than being played around with regarding the ship. I've learned most shows are not going to put the two leading characters together until the very last minute if at all. That's why I prefer the secondary ships like Bud/Harriet.