Owen Hunt (Kevin McKidd) has always wanted children. It was the biggest source of strife in his previous relationships because he kept dating people who didn't want kids. Now he has two babies, and while he would probably be thrilled to have another one, Owen is not the father of Amelia's (Caterina Scorsone) baby on Grey's Anatomy — unless the show is gonna throw audiences a total curveball.
Amelia discovered on the Grey's Anatomy season 16 premiere that she is likely pregnant. OB-GYN Carina DeLuca (Stefania Spampinato) took one look at Amelia and guessed that she was carrying a child. Presumably (hopefully) Amelia got a real test performed after that, because, in the promo for the next episode, she tells Link (Chris Carmack) that she's pregnant. It would be kind of a major misstep if she didn't have a test to back up Carina's guess by the time she tells Link — but who knows?
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In any case, the fact that she's telling Link at all is a huge sign that Owen is not the father. Amelia knows who she's been sleeping with, and it's Link. If there was a chance he wasn't the father, the promo probably would have showed her wrestling with that potential issue. Instead, she asks Link, "Can we go somewhere private?" He asks, "Bad private?" and Amelia answers, "Uh, I'm pregnant actually." Link doesn't quite know what to say to that, but viewers will see his full reaction in the Oct. 3 episode.
Amelia and Owen broke up in episode 15 of season 15. That was almost half a season ago, and five weeks passed in the season 16 premiere alone. Amelia can't be very far along yet if even she didn't realize she was pregnant. In those five weeks that passed, she was still only seeing Link and Owen was pretty busy raising his baby with Teddy (Kim Raver) and putting his and Amelia's house on the market to finally put that chapter behind him. It's extremely unlikely that Amelia and Owen had some sort of slip up and slept together while all of this was going on. Part of the reason Amelia broke up with Owen in the first place was because she was tired of being trapped in the Teddy and Owen triangle. Why would she have willingly re-enter it?
If the baby is anyone's, it's probably Link's. That storyline will test the strength of their budding relationship, both because Amelia wanted to take things very slowly with him and also because she's voiced in the past that she didn't want to have any more children. (She lost a baby years ago on the spinoff Private Practice.) The Owen and Amelia storyline is old and tired, having been fully explored in season 15. Owen has his two children now and his life with Teddy. There's no need for either Amelia or the writers to go back down that path.
Since that's pretty much cleared up, the real question is how is Link going to react and what will Amelia choose to do? Now, those are some unique, original storylines for these characters to explore.