The Showtime drama's first season concluded with Carrie realising that Brody knew Nazir's dead son Issa as she underwent mind-altering electroshock treatment.
Asked if Carrie will stumble across the revelation again, Gordon replied: "Absolutely. It may not come back to her exactly the way you'd imagine it might, but yes, that information will most likely emerge at some point."
On whether Brody will remain loyal to Abu Nazir following his election to congress, the showrunner told TV Guide: "Things are not binary, they're not just black and white.
"Often the most wonderful drama is this nuanced tug of war inside the characters in terms of why they do what they do. Honestly, one of the great delights is confusing or confounding expectations.
"No-one is all good and no-one is all bad. Everyone is hopefully explicitly and complicatedly human."
Gordon also confirmed that season two will pick up six months after the first and be set against the backdrop of an Israeli bombing of Iran.
The latest Homeland revelations come after the unveiling of a trailer for its second season at this year's Comic-Con.
Homeland will return to Showtime on September 30 and air in the UK sometime afterwards on Channel 4.
Watch Digital Spy's recent interview with Homeland's Howard Gordon below: