At first, it seems like Barry’s values have shifted since he had a son, but he quickly reveals his true colors. The thing about John that’s most important to Barry is his opinion as an audience member in the performance of a lifetime.
“The thing that was nice about him having a kid is Barry had a chance to be the person he always wanted to be in the eyes of his son, which is a hero and a guy who does the right thing and a guy who’s not violent,” Hader explained to The Wrap in early May. “This kind of upstanding American guy, which is a character he’s playing. So they’re still acting. It’s this idea of him being this upstanding person, but now he has this kid, and this kid can see him and reflect back the person he wants to be, and that’s really important to him.”
This is the integrity he seems to be protecting — not the safety of his family, but his moral righteousness in his son’s eyes. He abandons Sally and John to hunt down Cousineau when he poses a merely existential threat to them, and Barry even admits that his only reason for trying to kill the old man is that he doesn’t want John to know the truth. Barry is desperate to stay in character as his own ideal man, and now that his son is in Hank and Fuches’ grasp, his image will definitely be compromised.
It’s clear that there won’t be a happy ending for Barry, but there will probably be a bloody one. The only thing that’s certain is that he’s out for vengeance, and when that guy’s on the warpath, his enemies should probably get out of the way.