Geppetto does the hard thing and tells Snow and David that the tree can carry two.
Mortally wounded, held off from the Nursery by Regina's guards, desperate to save Emma and yet unwilling to leave Snow to the curse alone, David instead travels down to the dungeons and releases Rumpelstiltskin in a desperate bid to have him take Emma through the tree.
Faced with the hard choice of leaving behind his magic but being able to get to the World Without Magic and begin his search for Bae 28 years early, Rumple decides to gerry-rig a situation where he's "part" of the curse, but already outside it where it doesn't hurt him if he "leaves Storybrooke."
Rumple raises Emma as his adopted niece, not keeping the truth of her parents from her since he learned his lesson as Bae's father, and raising her to know her destiny and her history and what she's supposed to do. (It's the least he can do to repay David for putting them all in this position and the 28 year head start.)
Rumple is still, unintentionally, quite a bit like Mother Gothel to Emma, knowing as he does how precious and powerful she is. Between that and Emma growing increasingly skeptical of her "destiny," she runs away for a year at 16/17.
As a runaway street kid, she meets up with Neal, and her year with him happens. She doesn't tell him about her "crazy Uncle Gold", he doesn't tell her about his history.
With no August/Pinnochio to scare Neal away, Neal goes to fence the watches and gets caught and arrested. Emma--having waited for him for several hours--starts freaking out, feeling abandoned and that everything Rumple warned her about the world was true.
She calls Rumple in a panic who comes to pick her up and take her home.
Emma finds out later that she's pregnant and Mr. Gold, in order to give her some closure, comes forward with the article about how Neal had been arrested. Without magic aiding him and confirming that Bae = Neal, Rumple doesn't recognize his son.
Instead of getting closure like Rumple thought she would, Emma argues that Neal never meant to abandon her and begs Rumple to go get him out of jail and tell him about the baby.
Rumple agrees on the condition that he talk to the boy first while she waits at the hotel. What he's actually doing is going to question this "Neal" about his relationship with Emma and feel out if he is in anyway worthy of "The Savior" (And Rumple's little girl, shhhhh).
What Neal sees when he's told he has a visitor is his (human) Dad, glaring at him from across the table.
There's a bit of miscommunication and cross-talk until Neal kind of accidentally lets the cat out of the bag by assuming Rumple knew Neal was his son and trying really really hard to confirm that Emma is NOT in fact Rumple's biological daughter.
Things kind of break down and come to a head, then they all go home to try and repair relationships and build a family.
Regina has not been idle all this time. She may not be able to physically hurt Rumple or go after him and Emma, but she can threaten him. She does, after all, have Belle.
Early on, she had called Rumple to try and threaten him into giving her Emma, warning him that she had Belle and would hurt her in some way if he didn't. Rumple used quick thinking and the detail that he technically never violated the terms of their deal in order to use his "please" against her so that she wouldn't hurt Belle. Physically, Belle is safe.
In order to hurt Rumple though, Regina decides to give Belle her Storybrooke life back: a scantily clad barfly named Lacey, who's dating a one handed rum-soaked wharf smuggler named Kelly. It's even rumored that Kelly is the one who had scared Mr. Gold off from the town, forcing him to collect rent remotely, because Mr. Gold was trying too hard to steal Kelly's girl.
Regina stays quiet about all this, knowing if she calls Rumple to gloat, he will use his "please" against her again and actually force her to be nice to the girl. In the meantime, she gets what pleasure she can from it and stays under the radar. Rumple doesn't trust her, of course, but he's busy with other things and it kind of moves to a back burner.
It's around Emma's twenty-first birthday, when they're watching a few Disney movies with baby Henry that Rumple starts thinking about Belle again, seeing her, trying to fix things between him and her and Regina.
Rumple tells Neal and Emma of his plans, travels back to Stroybrooke, and settles into the routine he was supposed to have had to begin with.
Side effect of coming in from outside with the curse already on him is that it has a very slight weakening effect where Neal and Henry come to visit occasionally but something always comes up that keeps Emma away.
More shenanigans occur during the seven years or so with Lacey and Rumple and Regina and Henry and "Kelly" (Killian.) It comes to a head on Emma's twenty-eighth birthday where things ramp up quickly between a drunk Killian and a sober Rumple over Lacey and it ends up with them in the hospital. Emma and Neal are called and they finally manage to come to town.
I haven't decided where it goes from there, but, thoughts?