Perhaps Henry ends up getting sent to Neverland alone, maybe courtesy of Rumple, and becomes press ganged into being one of the Lost Boys. He would then meet Peter Pan. Whereas Peter and the Lost Boys want to stay young and play in Neverland forever, Henry wants to go home and grow up. Since Peter nad the Lost Boys are anti-adult, it wouldn’t make sense for Emma and company to be with Henry.
However, since Emma doesn’t want to leave Henry in Neverland, she finds a way to get there with Neal. Hook tags along too as their guide. Bae, perhaps being a former lost boy, would know where Peter’s hide out is whereas Hook doesn’t. Both Hook and Neal would have to go because Hook has the means to get to Neverland (his ship enchanted with fairy dust) and Neal would have the local knowledge (where Peter Pan’s hideout is).
During the course of season 3, the CaptainSwan/Swanfire triangle can play out with Hook and Bae trying to one up each other in Emma’s affections.
I like this theory, but I’m going to put my own spin on it. Given Henry’s hate for magic and mistrust of the adults in his life, I can see him running away to Neverland (perhaps just like his dad did). What if Henry stills a bean or hitches a ride with a fairy (following the immortal directions to Neverland)?
As for Emma and Bae going to Neverland to look for Henry – I like this. I also like Hook being their guide through Neverland. However, I think Hook is a grown up Peter Pan, which will be explain in season 3. So when we get to Neverland in the story’s present, I think Pan will be long gone.