I have a feeling Brody and Natalie aren't done. Not even when the truth about baby Liam is revealed. The writers seem bent on making Jessica/Tess and Robert a go, and have been steadily phasing him out of Jessica's orbit and into Natalie's. I'm sure Brody will be involved with a reemerged Jessica for a minute until it becomes clear to him there is nothing left for him there.

Meanwhile, I predict that Natalie will remember that John is Liam's father, but the two will feel hold on telling Brody–simply because it would leave him with nothing. From there, Brody will continue to dance around Natalie, while he exert his 'paternity' over Liam; and we'll end up with a John/Natalie/Brody triangle.