I decided to create an alternate ending as I was unsatisfied with the last one.
JJ was thumping Dean weakly on the chest in a final battle to get back to her brother as they entered the factory. Dean held her close as she fell quiet except for the sound of the sobs that racked her body. He placed her gently on the floor before moving quickly to the other the monster that was lurking in the background, Dean tackled the thing and Sam stabbed it with the metal, smiling when the creature crumbled. A gun shot rang out over the factory and the brother's turned quickly to see JJ slump onto her back, blood pooling around her abdomen.
'JJ! NO!', Dean shouted, sprinting to her side and ripping his shirt off, pushing firmly on the bullet wound. Sam dropped down next to him. JJ laughed and a smile spread across her face which was quickly paling.
'JJ. Come on. Stay with me. We'll get you to a hospital.', Dean soothed.
'No, I don't want to. I'm happy now.', She sighed, her voice weak.
'JJ. Come on.', Dean ordered, his breath misted the air and he looked up at Sam, eyes wide. Sam was gazing away from JJ and Dean followed his line of sight. A ghostly man stood on the factory floor, watching JJ.
'James?', Sam gasped, watching the ghost flicker slowly towards them.
'They told me to come get my sister, that I could help her.', James said, his voice echoing and cold. He leant over JJ and placed a hand lovingly on her face. Her eyes glassed over and the men gasped when James' hand came away with JJ's own ghost attached.
'I found you!', JJ whispered, flinging herself around her brother, a bright light shone out from them and a warm wind flew around the factory, disturbing the dust. JJ and James flickered in and out of sight, the light getting more intense with each second that passed before a dazzling light forced the brothers to shield their eyes. When they opened them, the ghosts were gone and the dust was settled.
'We'll give her and her brother a hunter's burial.', Den murmured, carrying JJ's lifeless body down into the basement and gave her to her brother, Sam followed with the bodies of the monsters.
They drove off just as the smoke became visible over the warehouse. Sam was curled up against the wheel, deep in thought.
'There's nothing we could have done, Sammy.', Dean soothed, patting Sam on the knee quickly. Sam just nodded and went back to his thoughts.