This week's episode shocked viewers by revealing that Robin (Cobie Smulders) is pregnant, but Bays said that there are "more revelations in store".
"I would say the wheels of fate are not done turning for these characters, and it's definitely a big surprise, but there's more to come," he told Entertainment Weekly. "This little story isn't over yet."
Bays explained that fans will find out the father of Robin's baby soon and hinted that "a bigger story" is on the way.
"New questions will arise and I feel like, this story, we are using this device a little bit to set the stage for a bigger story that is setting up the events of the rest of the series," he said. "This in particular is going to lead to kind of a reshuffling of the group. Not necessarily in this next episode, but this episode will set things in motion for that."
Bays said that there will be some "rocky events coming up" with Kevin (Kal Penn) and hinted that the story between Robin and Barney (Neil Patrick Harris) is "not done being told".
"There will be some developments," he teased.
How I Met Your Mother airs on Mondays at 8/7c on CBS.
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