"It's been a long journey, let me tell you," Emily told The Morning Show.
"It's like a real marriage. We have been doing a lot of sad stories, with the hospital siege and then Marilyn having PTSD."
She went on to say that that the current emotional storyline was a "natural progression" for the pair.
"We didn't need to prepare because the relationship had been disintegrating for quite a while,” she told hosts Larry Emdur and Kylie Gillies.
"It's very sad because the joyous and funny scenes that we’re used to do have all dried up."
In scenes that went to air this week, Marilyn and John were given one last test as their relationship issues came to a head.
Newcomer Amber had the potential to build a bridge between the pair, but in reality it only exacerbated the inevitable.
"Amber's arrival is a breath of fresh air into a tired relationship...although she gives as good as she gets," actor Shane Withington told TV WEEK.
Marilyn is grateful for the help, but admits to Roo she still feels helpless.
At home, Marilyn finds John has fallen over and races to help.
But instead of berating her, as he's been doing, the couple share a tearful exchange and admit that things just aren't working.
"John very bravely can see that Marilyn isn't happy and that it's not working," Shane said.
He added: "Perhaps it's time for both to go their own way and pursue their own goals and values."
Eventually, Marilyn came to a tricky conclusion by deciding to move out of their home they shared together.