I saw a couple of headcanons about Ed dying from the same illness his mother had, so this is my take on how he would say goodbye to Winry. AU. Sorry if it's depressing.
Edward Elric had just done one of the hardest things he has ever had to do, and he was about to do it again. He had just told his four children goodbye. Before that, he had said goodbye to his younger brother. Now, he had to tell his wife of seventeen years goodbye. He knew he was going to die. The doctor delivered the news that he had developed the same mysterious illness his mother had fallen to. A week ago, the doctor estimated that Ed would have ten days at the most to live. He told Ed to say goodbye to his family as soon as he was ready. Although Ed felt very weak and useless, he managed to hold his sons and daughters one last time. After holding his youngest daughter until she fell asleep, he finally felt the tears leak from his eyes. Winry had come to take their daughter away.
She returned a few minutes later to find Ed wiping his eyes. "Oh, Ed… how are we going to do this?" She asked her husband. Ed shook his head and whispered: "Come here." Winry walked over to the bed and stood to the side. Ed sat up and patted the spot next to him. Winry didn't make a sound as she lowered herself on the bed next to him and gently rested her head on his shoulder. He put his arm around her. Winry started sobbing. "Shh… Win, please don't cry over me. Re… remember our promise all those years ago." "I know." She said between sobs. "Winry." Ed said in a serious tone. Winry pulled away to face him. "I love you… so much. Thank you for everything you did, taking care of my automail, giving birth to our kids and loving someone like me." His voice broke on the last words. "Ed… I love you more… more than anything. Please don't leave me. I can't…" She stopped when Ed put his lips on hers for one last kiss. It was passionate, even though he had very little energy. Ed pulled back and rested his forehead against Winry's. "Let me stay the night… I just want to sleep next to you one last time." Winry begged him. "No, I won't let you be haunted by this image of me forever. I don't want you to hear my last breath." "Oh… okay… but can you hold me one last time?" She asked him. Ed took a deep breath then he slowly lowered himself so he was lying down. Winry gently pressed her face into his chest and Ed's arms came around her. He felt his shirt get wet with her tears, which made him start crying again. He didn't want to die and leave everyone he loved behind him. "Edward." He heard Winry's voice muffled voice in his chest. Ed's hand ran down her hair, trying to soothe her. She rose from his chest and held herself over him. "Edward. Thank you for all the years you've given me. Thank you for being a great father… and husband. I love you… forever." Ed took another breath and whispered: "Winry, I love you… always. Goodbye." Winry nodded and slowly got off the bed. She didn't turn around to look at him one last time, but he heard her sob before leaving the room and closing the door behind her. Hours later, right before he fell asleep for the last time Edward sobbed as last thoughts were of his family. He passed away in his sleep, free of pain.