The showrunner revealed that Nate's murder was intended to teach lead character Michael (Jeffrey Donovan) that his actions "come at a cost".
"A big emphasis this year is on the idea that Michael's quest to deal with all of it - whether it's being burned or going after Anson (Jere Burns) - that all of these things come with a cost," Nix told TV Guide.
"This stuff deeply affects Michael and drives him to do a lot of things. If you thought he was driven before, man is he driven now. And there's a cost to that as well."
Nix further explained that Nate's death will challenge Michael's inherent desire to get even.
"It's easier for Michael to risk his life for you than it is to say he loves you," he argued. "So when his brother is dying, what is his instinct? To somehow make it okay, and that's a big part of the second half of the season.
"He's trying to redeem something that's unredeemable. He's trying to make his brother's death okay, but no amount of hunting and avenging makes it okay. None of that brings Nate back."
Burn Notice returns to USA on August 2.