This takes place right after season 5, and is thus a theoretical season 6. Hook is back from the Underworld, Robin Hood has died, and Mr. Hyde is in Storybrooke with the goal of joining his world with Storybrooke and ruling over the new land. Furthermore, Regina has separated herself from the Evil Queen.
EPISODE 1: SLEEPING SWAN
Emma was curled up next to her pirate in the home he had chosen for them back when she was still the Dark One. A pale blue light streamed gently through the window and Emma stared out across all of the shadows in the room. She couldn't sleep, a problem Hook certainly didn't share, judging by the rhythmic snoring and loose grip of his arm around her stomach.
Mr. Hyde had been in Storybrooke for three days already, making his plans. The gang hadn't been able to figure out his endgame yet, and hadn't been able to stop him, either. They had tried, but some sort of magic protected him. He had claimed to be the new owner of the city, by Mr. Gold's doing, and as such seemed to have certain powers there.
Emma had tried to reason with him, to no avail, and when she realized her family was in danger, she made to end the beastly man. Two bullets shot through his flesh, and he faltered, appeared to die, and then rose again.
"You cannot be rid of darkness so easily, Mrs. Swan," he had crooned with a sneer. "This is my town now. You cannot stop me."
Emma shuddered now, thinking back on his cruel tone and the evil in the man's eyes. She shivered, but felt too warm—the blankets and Hook's body heat, it was all too much warmth for her. With a gentle grip she raised Hook's wrist up off of her stomach and dropped his arm gently at his side. Slowly, as not to wake the sleeping pirate, she rose off of the bed and tiptoed out of the room.
In the pale moonlit rooms downstairs Emma paced slowly about, unsure of what to do with herself. She was too anxious for sleep and had too much on her mind.
There was the new big bad to contend with, of course, but she had an inkling in the back of her mind that there was more to her discontented state. Hook was back, and she was thrilled. Still, she felt guilty. Again, because of her family, Regina had lost her love. Emma hadn't seem much of the former Evil Queen in the past few days, and found herself missing her friend, and still feeling guilty for assuming she would so easily resume being the Evil Queen she had once been.
The Evil Queen though—she was dead now. Perhaps Regina could finally find her happy ending, and without that darkness holding her back, perhaps, Emma secretly hoped, they would be able to forge an even stronger and more stable relationship. Emma had always believed in Regina; she had stood beside the mayor long before the mayor had grown to believe in herself. Sure, they had had their rivalry when Emma had first arrived and Regina was fearful of losing Henry, but since then the mayor had become a close friend, and family, and together they worked to raise their son and find Regina's happy ending.
But Emma had accidentally caused Regina to lose that happiness that she had found with Robin Hood. Because of Emma wanting to go to the Underworld to save Hook, Hades had been able to kill—no, worse than kill—Regina's soul mate. And with Hook back, Emma wasn't really able to console her friend, who instead found solace in her sister. There was a twinge of jealousy for Emma, and she shook her head with a frown, disgusted at the selfishness of her thoughts.
Emma rubbed her temples and willed back the dampness that formed in her eyes. She wanted to make up for what she had done, but didn't know how. She had caused the death of her dear friend's love and then been so idiot as to lose faith in her right when Regina needed her, when Regina was hurting and needed her friend. But, what could she do? She felt all the worse because of Hook; she was glad for his return, but it didn't seem fair.
The sheriff glanced at a clock on the wall to see that it was a little passed four in the morning, not too strange of a time for her to take a walk. Without even bothering to changed out of her pajamas, sweat pants and a tea shirt, she donned her red leather jacket and crept outside into the cool summer night. Maybe a jog would help her clear her mind.
The cool air felt wonderful on her just-damp skin as she turned around another corner almost an hour later, having toured most of the city already. She had stopped for a bit where Henry's castle used to be, to think, but only for a short while before she had taken off once more through the nearly vacant town.
She now found herself on Mifflin Street in the wee hours of the morning, the town just beginning to grow a bit brighter with the oncoming day. Emma slowed to a sluggish walk, unsure of what it was she was doing. She had felt drawn here, and had circumvented it for the duration of her run, but now—here she was, just down the street to Regina's home. At first, she thought perhaps she had wanted to talk to Henry, but as she walked the dark road, her thoughts fell instead on her former nemesis. There was a solemn tug at her heart, a pang of desire to see Regina, to sit and talk with her, to somehow glean that she was all right—that they were all right.
She knew she couldn't very well go knocking on the mayor's door at such a time, but still she didn't stop her slow pace towards the Mills House and once there, into the yard. Instead of heading towards the front door, she turned instead to walk around the house to Regina's prized apple tree. She had cut down this very tree once, back when she and Regina were at constant odds, but it had regrown with the arrival of magic.
Emma sat on a bench in the small courtyard, admiring its dimlit beauty, staring fondly upon the tree, as if it stood as a testament to Regina herself, and her strength to withstand and regrow.
The sheriff rubbed her arms nervously, still unable to ascertain her own reasons to being there on the Mills property in the early hours of the morning. She knew that a part of her wanted to speak with her friend, to see her face, but it's not like she would actually go knocking on the door, so why was she still here? She sighed and hid her face in her hands. She should be at home, with Hook, not sitting there in Regina's yard.
"Miss Swan," said a voice that somehow both snapped and sang. "What are you doing here?"
Emma jumped to her feet in a scramble, turning to face the source of the voice. "Regina, I-" she began, but stopped when she saw the woman before her.
It was the Evil Queen standing before her, staring her down with a curious smirk on her face, her hands and their magic held at the ready.
"No," Emma stammered, "this can't be. I watched Regina crush your heart. You disappeared…"
The Queen threw back her head in a haughty laugh. "Haven't you learned, Miss Swan? It isn't so simple to destroy darkness. I can't be destroyed so easily."
"Wanna bet?" the sheriff retorted, the sharpness in her voice conveying a confidence she did not actually have. She held up her own hands and held her own light magic there, ready to strike.
The Evil Queen laughed once more. "Do you really think you can stand up to me?" She smirked when Emma narrowed her eyes in response. "Unlikely."
Emma watched the other woman cautiously as she began a slow circle around the sheriff.
"Are you in your pajamas?" the Evil Queen asked with a sharp laugh, her cruel, teasing tone causing Emma to flush in embarrassment. "Hmm," she continued. "It's been awhile since I've looked upon you. I think. You know, it's sort of hard to tell when I ended, exactly, when I lost control." The Evil Queen looked away from Emma and towards her—Regina's tree. "Her memories are mine, but they also aren't. It makes me sick," she snarled. "We became so weak. All this love business. You just had to convince us, her, that we deserved love. Look where that got us. Got her."
Emma swallowed hard, her ears burning with shame. "It wasn't meant to happen like this," she mumbled.
The Queen laughed and turned back to the sheriff, her dark eyes glittering. "Of course not, Miss Swan. It was meant to be a happy ending, was it not?" She shook her head. "That isn't for us. That's for you hero types."
"You-she...Regina is a hero," Emma defended.
With a scoff, the Evil Queen glared Emma down. "She's weak, that's what she is. I'm here to put an end to her at last, so we can stop ignoring our destiny. She gives me a bad name."
Emma's heart was pounding. "I won't let you hurt her," she declared, raising her hands higher. Henry needs her, she thought. We need her. I need her.
She shook her head at that last thought. Of course she needed her, they all did. She was part of the team. They wouldn't succeed without her. She was Emma's friend, and Emma cared about her.
The Evil Queen raised a brow, wondering what was going through the sheriff's mind. "I suppose you wouldn't," she snarled, "what with being the Savior and all."
Emma fumed. "This isn't about that. Regina's my friend and I won't let you hurt her."
The Evil Queen had walked away from Emma and towards the apple tree. She reached calmly up and plucked an apple off a branch. "Friend," she muttered impatiently. "Right. Is that why you always put your needs first? Is that why you chased after your beloved and got ours—hers killed?"
Emma, despite herself, glanced away in her shame. "I never meant for that. I'm sorry."
"Don't apologize to me, Miss Swan," she responded with a sneer, sauntering back towards the sheriff. "As I said," she leaned in close, and Emma could not refrain from looking towards the woman and into her dark eyes.
Emma gulped.
"Love is weakness," the Evil Queen stated calmly. "And don't worry," she added, leaning back once more, smirking when the blonde sheriff took a deep breath, "I'll put her out of her misery."
She made a gesture as if to magic herself away, but Emma quickly grabbed hold of her wrist.
Emma, bristling, snarled, "No, you won't."
The Evil Queen briefly lost her confident smile, and she stared Emma down as if to study her. "Do you realize who we are? What we've done? Sure, she's separated herself from me, but does that really excuse her for all the lives we've ruined, the people we've killed? She was me, we were the same person. We did those atrocities, together. Let it go, Miss Swan. Heroics and happy endings aren't our thing. I'm going to set this right."
There was something strangely earnest in the Evil Queen's voice, something that seemed to be genuinely asking Emma to let her go, as if what she was about to do was the right thing. She sounded more like the Regina Emma knew, the one she trusted, and she nearly let go before coming to grips with what would happen if she did.
"Over my dead body," Emma snapped.
The Evil Queen growled, and in a sudden, quick movement, shoved her hand into Emma's chest. With a painful tug, she ripped out the heart that beat therein.
Emma gasped in both pain and shock. Her eyes went wide with fear.
"You've become quite the nuisance, Miss Swan. I think it's about time I put an end to the "Savior" and get you out of my hair once and for all." She tightened the muscles in her fingers, prepared to crush the pulsing heart in her palm, but found that, for some reason, she could not bring herself to do so.
"Can't do it?" Emma taunted, her tone just barely betraying the fear that nearly rocked her legs beneath her.
"As if," the Evil Queen responded coolly, covering her tracks. "I merely thought that perhaps there would be a better use for this." She sneered.
Emma grimaced. "Give it back," she muttered, "it doesn't belong to you."
The Evil Queen laughed. "Are you so sure? I do hold it in my hand, after all."
For some reason unbeknownst to her, Emma blushed slightly, and hoped that the oncoming daylight was not yet bright enough to betray her.
"I control you," the Evil Queen declared. She gave a laugh. "You're mine." She raised Emma's heart up before her face and gave it a slow kiss, causing Emma to blush even more. With her other hand she raised the apple she had plucked from the tree.
"Perhaps," she considered, "I could have some fun before I go killing the only people left in town." She raised the apple to Emma's lips as purple magic sparked at her fingertips. "Eat," she crooned, staring intently into the blonde's emerald eyes.
Emma stared back into the dark eyes of the Evil Queen and saw in them something familiar. They were Regina's, but with an unchecked darkness within them, and yet, as she stared into their dark hues and heard Regina's voice command her, she felt herself pulled towards obeying. She trusted Regina, and that instinct was there, grappling with the one that reminded her that this was not the same woman she had come to call her friend.
"Take a bite, Emma," the Evil Queen whispered softly into the heart she held within her hand, forgoing the usual colder titled with which she usually addressed the other woman.
Emma could no longer resist. She parted her lips, biting slowly into the apple being offered to her. Its juices dribbled across her lips and down her chin. Her eyes grew heavy and fluttered shut, closing on the image of Regina's—no, the Evil Queen's face grinning triumphantly over her.
"Regina…" Emma called out weakly.
"Emma!" Regina's voice called out in a panic, softer and more earnest than the one she had just been speaking to, its sharp but genuine tones echoing across Emma's mind as the last shred of consciousness flowed away.