I think I am going to go with the amnesia and Huley plays friend to him the whoops on him for killing Libby...

Or we find out Libby was Dharma or something and they have to thank him for knocking her out before she could do any damage..

__________________
Please don't give up, Des. Because all we really need to survive is one person who truly loves us. And you have her. I will wait for
you. Always. I love you, Pen

DESMOND: I love you, Penny. I've always loved you. I'm so sorry. I love you!
PENNY: I love you too.
DESMOND: I don't know where I am, but--
PENNY: I'll find you, Des--
DESMOND: --I promise--
PENNY: --no matter what--
DESMOND: --I'll come back to you--
PENNY: --I won't give up--
BOTH: I promise. I love you.