("White Out"), Assembling her first conference as mayor in her new office, Mary Margaret holds Neal while beginning the meeting as she introduces the townspeople to her discussion points on the listed agenda. As a means to purposely avoid each other, Mary Margaret comes to the diner at seven forty-five in the morning when David suddenly walks in. When she announces that Prince Charming has been taken by King George, they offer to go with her to save him. Jasmine suggests that David use his second wish on the lamp to undo his and Snow's curse, but David declines, out of fear that this wish will backfire as his first one did. Then, after Cora followed them back, she killed one of Mary Margaret’s oldest friends and revealed that she was responsible for her mother’s death. Emma advises for trusting her instincts—if it felt wrong, it probably is. Eventually, she is cornered at a cliff, but jumps headfirst into the water to elude capture. Snow is apologetic that he is losing the last of his family, but Charming is grateful to have her as his wife since they will have children of their own. Jekyll is too terrified to help them, but before he can make them leave, an orderly named Poole arrives to magically taser the group into unconsciousness. One day, she is teaching her students to make bird houses and tells the kids to make them with care, as they are building a home, not a cage. Though she believes this makes herself weak, her mother is very proud of Snow White's sign of strength and goodness. After entering the Netherworld, Mary Margaret waits in the flame filled room for Henry, but is stunned to see David instead.

From this leap of faith, Prince Charming is revived just as the curse closes in. Snow and the heroes investigate the clock tower, where they learn the tremor resulted from Mr. Gold tethering Storybrooke's magic into a piece of the Olympian Crystal. They have a brief reunion just as King George's men kidnap Prince Charming, though she promises to rescue him. A worried Emma arrives to heal her mother, leading to a reconciliation, as she forgives Mary Margaret for her past mistakes. Later, Snow receives good news from Dr. Whale, who reports that the surgery went well and the man will recover.

The two leave and reach an intersection where they must part.

("The Doctor"), Mary Margaret volunteers to go up the beanstalk; citing herself as more familiar to the Enchanted Forest than Emma. As they all leave the station together, Belle runs up, reporting that Mr. Gold is missing. While the soldiers are checking the tree, she snatches a bag of jewels before fleeing on horseback.

She admits Snow was right and this man isn't her Robin, but this leads her to question why Robin was able to come through the portal to Storybrooke if it wasn't to start over with her. Alive After birth, she and Prince Charming have a shared moment with Emma until realizing that their child must go through the wardrobe alone or all is lost.