Our Song - Background Information:
What if Emily and Aaron got together after those seven months of hiding from Ian Doyle to protect her?
During her fight with Doyle, Emily was sent to the hospital after being stabbed by Ian Doyle and had JJ and Aaron keep Emily off the radar to keep her safe. Jack and Aaron visit her from time to time, after Haley passed away Jack and Emily got really and babysit Jack for Aaron sometimes.
With Emily gone for those 7 months, Aaron kept her to date with everyone on the team and how they are doing after her being gone. Only Aaron and JJ know that she's alive, they thought it was best to keep it minimum just for her protection so that Doyle won't find out that she's alive.
Between those months of being away and having Aaron by her side through all her nightmares, they eventually fell for each other and Doyle showed up at Declan's school, it was time that Emily returned after her friend called her that Declan called him. The team finds out that Emily was alive the entire time and went undercover in order to protect her from Ian Doyle.
Emily and Aaron decided to keep their relationship a secret until it was the right time to come clean about their relationship to the team and Strauss. They didn't know if they'll support their relationship and how Strauss will take their agents dating each other and how it'll affect the team, or putting them in different departments.