This takes place during the crossover "Crisis On Earth-X". Barry and Iris were gonna get married but were interrupted. During the battle, Thawne got curious and decided to search Barry's home. What he did next was unpredictable.
Barry sped away to his home. He took Iris with him to their loft. Even though they were in battle with the Nazis that had invaded their Earth, Barry didn't forget about his baby girl he had at home. Her name Jo Bree Allen, named after her grandfather Joe West. She was kept safe away in her crib.
Iris got pregnant around January. Barry was really scared with what was going on with Savitar. He didn't want to lose both his girlfriend and baby at the same time. After Savitar was defeated, Barry went into the speedforce and missed half of Iris' pregnancy. But as soon as Barry got out he decorated the nursery and prepared for their baby. He was so excited to become a father. A family with Iris, it's all he ever wanted. Then the day finally came.
*Flashback*
It was Thursday morning when Iris started feeling something. She felt a strong pain in her abdomen. Barry was no where to be found. He was on a mission with the legends and Oliver. He wouldn't be back for a while though.
"Baby girl, not now please," Iris said as she rubbed her belly, "daddy isn't here yet. Just hold on a little while more."
As the day went by things when by a little smoother until the clock struck noon. That's when Iris felt a tremendous pain and she just could hold it anymore and decided to call Barry. The phone rang.
"Iris? Is everything ok?"
"Babe I know you're busy and you said to call only in an emergency."
"What's worng? Are you ok? Is the baby ok?"
"I was trying to hold it in but I just can't anymore. I think I'm in labor. I've been having very strong and painful contractions." She said. "Ok ok, just stay calm and breathe." As soon as Barry said that, Iris felt another contraction followed by a gush of water running down her leg. "Barry my water just broke, you need to get here! Now! It's time. The baby is coming."
"On my way." Of course he had to come up with some excuse but luckily the team bought it and Barry was off to Iris' side. "How are you feeling?"
"It hurts, the pain is getting stronger."
"Just breathe. I'm here, all right? I'm not gonna let anything happen to you or our baby."
They soon made it to the hospital and Iris was checked in. Barry didn't leave her side. Her labor lasted at least 5 hours. Then she came out. Barry was in love. He was now a father to a beautiful girl. His baby girl.
"You did it Iris." Barry said.
"No Barry, we did it. Look Barry she has your eyes. Big beautiful green eyes."
"She has your smile." Barry kissed the baby's forehead. "She's my princess."
*Present*
"Hi baby girl, it's your mommy." Iris picked up the tiny infant and cradled her.
"Iris I can't risk losing her. I don't think she should stay here."
"Barry it's ok. You've installed every kind of security ever made. Our daughter is safe."
"Are you sure? I can take her with Joe, far away from here."
"It's fine. You know this baby is lucky to have a father like you." Iris cradled the baby in her hands. Then Barry took her. "My sweet baby Jo. I love you so much. I'll see you soon my beautiful girl." Barry placed her back down into the crib. Made sure all the baby monitors were working. Security systems were all functioning well. Both parents kissed their daughter, not knowing it was the last time they would ever see her.
They left their sleeping baby in their house and returned to Star Labs.
"Anything?" Iris asked.
"I have a location." Felicity says. Barry turns his head towards Oliver and nods.
"Suit up." He says. Everyone got ready for a fight. They all geared up and put on their brave faces and headed out. Iris and Felicity were stuck in the cortex, bored. Iris decided to check the baby monitor.
"What are you doing?" Felicity asks. Iris completely forgot that her daughter was a secret from their friends.
"Oh, I forgot we didn't tell you guys."
"Tell us what?"
"Barry and I had a baby girl. We wanted to tell you guys but you know Barry. He's overprotective especially now because he's a father."
"How old is she?"
"A month old. Her name is Jo Bree Allen. Named after my dad. I'm sorry we didn't tell you and Oliver sooner it's just, we wanted to keep her safe you know."
"Don't be sorry, completely understandable."
"Thanks Felicity." Iris smiled.
Barry and Kara soon raced to the location and waited for Oliver. Unfortunately he did not have super speed.
"Super speed, I don't have it."
"Noted." Kara chuckles.
"Welcome. Glad you could make it." A woman in black leather said. Looking a lot like Kara.
"And who the hell are you?" Oliver demeaned.
"Well well well, if it isn't the Flash."
"Thawne." Barry said with hatred in his eyes. "Long time no see huh?" Thawne said.
"Not long enough."
"I just wanted to say congratulations on getting married. She's a lovely lady."
"You stay the hell away from her."
"No Barry, I don't want her, no... no no no, I have plans for the future. You'll see."
"Enough Eobard. Let's get what we came for." the lady in black leather said.
"Get off our Earth." Kara said.
"Not until we get what we came for." Dark Arrow stated.
"This is sick." Ollie said.
"Looking at your own reflection and only seeing weakness? I agree."
"Enough already. You ready Barry? Flash and Reverse-Flash at it again." Thawne said as his eyes turned red. Barry sped off after Thawne, as fast a he could. While the speedsters ran back and forth, Oliver shot Earth-X Kara with a kryptonite arrow.
"Is that a kryptonite arrow? Why do you have a kryptonite arrow?" Kara asked in shocked.
"In case an evil you ever showed up."
"Makes sense." Supergirl then threw some punches and used her laser eyes, but Thawne came and knocked her out and Barry, that left the Green Arrow all alone. "Felicity! I need back up"
"Hold on." She said, but it was too late. Oliver was soon knocked out by the evil Kara. As for the other heroes, they were no match for the Nazi-freaks.
Flash soon woke up to the Dark Arrow and evil Kara standing in front of them. Thawne was no where to be found. He was up to no good.
Through the walls of the West-Allen loft, came a man in a yellow suit. Eobard Thawne of course. He got curious to see what has changed since he last saw Barry Allen. A lot has changed. While searching through the house very carefully and quietly, he noticed a blanket on the couch. Not just any ordinary blanket. It was a baby's blanket, a baby girl to be precise. Then he noticed a picture with Iris and what appeared to be her in her pregnancy.
"A lot has changed, Flash. Let's go meet the newest member of the Allen Family." He walked very gingerly up the stars, one foot in front of the other until he made it to the baby's room. Thawne pushed back the door and there she was.
"Yes. You've got the Speed Force coursing through your veins. Just like your father. For now, no sign, no trace of the girl you will be in the future. I'm sorry for what I'm about to do, little runner, but you will understand I did all this for you, Prometheus."