Handsome Jack was a Hyperion programmer called John. He had the mask on already when he was at Hyperion and it seems his wife either disappeared or died. It could be that his daughter,Angel,did something as another recording implies a similar fate happen to a dozen other Hyperion employees too,and that is wife had suggested they stop what they were doing. I think the abuse by his grandmother and what happened to his wife drove him over the edge.
The mere mention of her made him murder an employee and it appears he already knew about Pandora when he was a programmer,which enabled him to get to the top of the Hyperion corporation. How would some programmer know about The Destroyer and The Warrior??
It seems The Warrior is a failsafe in case The Warrior was let lose,as it is activated by Eridium,which spread though the planet after the first vault was opened. I suspect the weapon the The Eridians used against The Destroyer was The Warrior.
Have you noticed the Cult of the Vault challenges?? It does make me think Handsome Jack might be linked to this.
Another aspect,Handsome Jack spared Tannis after he got the key?? It seems out of character for him,so I do wonder if Tannis,is linked with him someway?? She is obviously crazy,cannot handle people and interested in The Eridians,so I wonder if she is actually the mother of Angel,and was driven crazy when she was younger by her??
Have you also noticed how Sirens are important to open the vaults in both games?? It indicates that The Eridians seem to have some influence too.
Also,Handsome Jack does appear to love his daughter despite what he did to her,and maybe in his own twisted way he thought he was saving her??
This take on him is quite interesting:
www.destructoid.com/blogs/StriderHoang/handsome-jack-the-father-the-hero-the-ass hole-236158.phtml