Alex (Justin Chambers) has been struggling to move on since Izzie (Katherine Heigl) left the show during the last season.
However, Rhimes told Entertainment Weekly that finding closure for Alex will be one of the main priorities in future episodes.
"We're talking about it [in the writers' room] obsessively and trying to figure it out," she said. "We're approaching it pretty carefully.
"I want however we deal with Alex growing up and moving on and moving past that relationship to feel authentic and not to feel like something that's patched together."
Rhimes claimed that the storyline will not take "the expected form" but was unclear about whether Heigl will return to reprise her role as Izzie, saying: "I don't know."
The new season of Grey's Anatomy begins on September 23 on ABC.