This is set in Season 3 Episode 10 while Kara is in her coma. If Lena found out about Kara being Supergirl because of her absence.
(Third Person)
"Speaking of the kiss, have you seen Kara lately? She doesn't know that we kissed, we should tell her. Where is she?"
"She's... sick. She's got the flu, bad... flu. She's... at her apartment but... she's sick. Highly... contagious..." James stuttered, not expecting that he had to cover for his comatose friend.
"Why didn't she tell me? I'm her best friend!" Lena walked up to James, then had an idea. "You know what? I should go visit her. Make sure she's okay." She walked away but James stopped her as she reached the entrance of the office.
"Uhh, Lena?"
"Yes?"
"Super... Soup." James decided against telling Lena about Supergirl.
"Soup?"
"You know, she's sick. You should get her some soup." Lena nodded and smiled reluctantly. She left the office and headed for Kara's house, via the shops so she could grab some soup.
"Kara? Are you in there?" Lena knocked a few times but got no reply. She knocked again and this time, she got a reply.
"Lena?" The voice was quiet, but not from the person Lena expected.
"Where's Kara?" The door opened to reveal Alex, who was crying. "What's wrong?" Lena gave her a hug, which just made Alex cry more. They both walked inside and sat on the couch. Lena comforted Alex as much she could. The grief that Lena noticed in Alex's eyes was too strong to be anything small.
"It's Supergirl, she is in a coma." All this did was confuse Lena even more. 'Why would Alex be this distraught about Supergirl?' She thought, "Wait. You... you don't know yet, do you?"
"Know what?"
"Kara, she's... she's Supergirl."
Alex led Lena to the room in Mon-El's ship where Kara was inside one of the tubes that Lena had learned would eventually heal her.
"Kara," Lena whispered and put a hand on the tank. She thought she noticed Kara twitch a little but she told herself that she was seeing things. That is until Kara's eyes flew open and she started failing around and struggling to breathe.
"Lena, get ready. I'm going to drain the tank and open it. You need to be ready to grab her." Alex half yelled as she pressed a few buttons on a screen behind them. The tank drained quickly, leaving Kara still hyperventilating. Lena grabbed her friend as the tank opened, lowering her to the ground slowly while running her fingers through Kara's still wet hair.
Lena propped Kara's neck up for support with her arm. She noticed that Kara was starting to slip away again so she tried her best to keep her awake. "Stay awake, please. I can't lose you. I have something very important to tell you, what will I do if you die?"
"I'm sorry," Kara grunted and closed her eyes slowly.
"No, no. Please stay with me." Lena said as Alex ran to them and picked Kara up. She took her to a bed in the next room and hooked her up to some of the machines in there. This whole time, Lena had been holding Kara's hand.
"So, you come here often?" Lena tried to lighten the mood once Kara was more awake.
"Only for the comas," she returned the joke and tried to sit up. Alex rushed over to her and pushed her back down.
"You still haven't healed yet. You need at least a couple of days more of recovery."
"I feel great, really. Whatever injuries I got from the fight have healed."
"No, they haven't. Your ribs are still broken and we can't be sure that the lung which collapsed, is okay."
"Collapsed lung?" Lena gawked. She looked at Alex and then back at Kara. The blonde smiled and looked okay. "Just let her come back to her apartment, Alex. She'll be okay. I'll stay with her and make sure she rests."
"Fine. I'll get J'onn to take you two to Kara's apartment but you both need to promise me that she will rest." The two women nodded and got excited. Kara sat up and only now realised she was holding Lena's hand but she didn't say anything, knowing full well that Lena needed to tell her something and she had a fair idea of what that might be.
By the time they both got home, it was midnight. Lena helped Kara to bed and Lena went to sleep on the couch.
"Lena?" She turned around and knelt back down next to Kara. "Stay until I fall asleep?"
"Sure." Lena sat comfortably on the ground and holding Kara's hand.
"What was the thing you needed to tell me?"
"Um... uh..." Lena had no clue how to tell her. She hadn't actually thought of what she was going to say or how she was going to say it. "Kara, I know you are Supergirl."
"Is that seriously what you were afraid to tell me?"
"No..." Lena closed her eyes as she said the next sentence extremely quickly, almost too quickly for the blonde to recognise what she was saying. "Ihavefeelingsforyou."
Kara laughed and rolled onto her back. She patted the bed on the other side of her, signalling to Lena that she wanted her to lay next to her. The brunette followed her instructions and laid next to Kara, smiling as they rolled onto their sides simultaneously and face each other.
"I understand, Lena. More than you know."
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