The actor told TV Guide that Tony DiNozzo's romance with EJ Barrett (Sarah Jane Morris) will be strained in the CBS drama's ninth season.
Weatherly explained: "There's a new wrinkle in [their] relationship, and I would say it is somewhat troubling. I think Tony questions a lot of things about her, and I don't think there's any going back to their initial... lovey-dovey plot."
However, he also dismissed speculation that DiNozzo will get together with former love interest Ziva (Cote de Pablo).
"Tony ultimately has to lean on himself," he said. "He has to figure some of his own stuff out. That might make him more able down the road to approach a relationship with Ziva."
NCIS showrunner Gary Glasberg recently revealed that the new season will explore Ziva's past.
The show returns on Tuesday, September 20 at 8/7c.
> Jamie Lee Curtis to appear on NCIS
Watch a trailer for the NCIS eighth season finale below: