The flashback story I figure you have been waiting for. This is set when Nagisa is 5 and Rei is 9. It is around Spring time, about half a year (a little more) after Makoto adopted them.
Since 5 years old Nagisa had started school this spring he had thought school was fun, just like Rei had told him it would be. Although the teachers continuously reminded them that this was only kindergarten and that school would be much tougher once it actually got started, Nagisa couldn't help his believes.
Right now, Nagisa was sitting on a chair in the classroom, swinging his legs back and forth, because they couldn't reach the floor, while listening to their teacher talking about the hiragana and katakana. Nagisa knew of both. He had been taught in the orphanage and Makoto had also explained some more of it to him. But there were some in the class who hadn't learned them yet, and therefore their teacher had to start from the beginning.
The school day was nearly done when their teacher, Sakamoto-sensei changed the subject she was talking about to something entirely different.
"For tomorrow, I have some homework for you. It will be your very first homework," she said with a bright smile, like she had just given them some very good news. Nagisa noticed how the entire class smiled. Nagisa smiled as well. "Due to tomorrow you will have to make a family tree of your own family, that means your brothers, sisters, parents, grandparents, aunts and uncles, and cousins, as many as you can think up. Just draw a picture of them and write their names and their relation to you, like this,"
Sakamoto-sensei pulled up a paper and showed her own family. "That's me," she pointed to the bottom of the paper. "Next to me is my sister, here are my parents, and that's my mother's sister and her husband and son, and there are my grandparents," she pointed them out as she mentioned them. "Tomorrow you will present your families to the entire class,"
Suddenly homework weren't as much fun as Nagisa had thought they would be.
The following day, when they had Sakamoto-sensei again, the entire class was prepared to present their families for the others. Nagisa was sitting by a table with three of his classmates, Akito, Ayato and Yukio.
"I managed to make a really great one!" Yukio said while showing his to the other three boys around the table. "There's my older brother and my older sister is there, and there's my mother and her brothers and my father and his brother and my cousins, and here are my grandparents," he pointed them out as he spoke. "I get best along with my cousin Shun on my father's side," he said and pointed said cousin out.
"Mine's better," Akito said and showed his. "Look at it,"
"I bet you mine's better," Ayato said and showed his as well.
Nagisa and Yukio took a look at both family trees and a realization hit Nagisa after only a few moments. "Aki-chan, Aya-chan, aren't they mirrored or something? They look almost the same," Nagisa asked.
Akito and Ayato nodded and Ayato explained. "We are twins, so we have the same family," he said.
"That's so cool!" Yukio said. "I wish I had a brother my age!"
Both Ayato and Akito shook their heads. "No," Akito said. "You won't want that, we have to share everything! That's so annoying!"
Nagisa dragged himself completely out of the conversation. All he wished right now was that he had a family. Of course he had Makoto and Rei, but they weren't his real family. He wasn't stupid. He knew he had been adopted. He still remembered the time at the orphanage when it was only him and Rei. It was less than half a year ago since they were adopted.
"Alright class!" Sakamoto-sensei said. "Let's get started on the presentations. We take it in alphabetic order so be sure you know when it's your turn,"
When she said alphabetic order, she meant by the surnames, which meant Nagisa was in the latter half of the class. He therefore sat and waited and watched as his classmates went up to the front one by one and presented their families. Akito and Ayato did it together because they were twins.
Nishii Satsuki had just finished presenting her family and had headed back to her chair and the rest of the class was now waiting for the next to come up. But nobody came.
"Who is next?" Sakamoto-sensei asked.
Nobody answered and she had to look at the list of students to see who it was. She looked up at Nagisa as she finished. "Hazuki-kun, would you please present your family to us?" she asked.
Nagisa walked up in front of his class. His hands were empty.
"Where is your family tree?" Sakamoto asked as she noticed this.
"I didn't make one," Nagisa answered honestly.
Sakamoto sighed. "Sit back down, Hazuki-kun," she said. "You will stay behind after class and we will work on it together," she said.
Nagisa did as he was told. The rest of the class stared at him all the way.
Makoto was home from work. He had just entered and taken off his shoes when the phone started ringing in the living room. Rei was already home and he could hear the oldest of his boys go to answer the phone for him. Makoto silently thanked Rei for that. Sometimes he thought it was a huge relief to have both Rei and Nagisa in the house, even if they were still young they could do little things that helped him to not stress as much.
"Makoto-san!" Rei called from the living room. "Makoto-san, it's from the school, they want to speak to you," he said.
Makoto wondered what they wanted to speak to him about as he headed to the living room and accepted the phone, which Rei was handing to him. "Thank you Rei," he said before putting the phone to his ear. "Hello, Tachibana Makoto speaking," he said.
"Hello, Tachibana-san," it was a female speaking. "I'm Sakamoto Mayu, Hazuki-kun's teacher," she said.
Makoto nodded. "What is this about? Has Nagisa done something?" he asked.
"Sort of," Sakamoto said. "He has refused to make a family tree, the task is perfectly clear, I kept him here after school as we could work on it but he kept refusing, just now… Just now he started crying and I don't know why," she explained.
"I see," Makoto said. "I'll come to the school right away,"
Ten minutes later, Makoto and Rei were at the school and on their way down the hallway to Nagisa's classroom. Makoto opened the door and walked inside. By a table in the back the still sobbing Nagisa was found along with his confused and worried teacher.
"Nagisa," Makoto said and hurried over to the blonde boy. Rei kept on standing by the door.
"M-Mako-chan," Nagisa sobbed. He looked up and saw Makoto, and then his gaze landed on Rei and Makoto was long forgotten. "Rei-chan!" he exclaimed and ran to Rei. He jumped into the older boy's arms and sobbed into his chest, fresh tears started running down his cheeks.
"There, there, Nagisa," Rei said in an attempt to comfort the younger while patting his head softly.
"Rei, Nagisa," Makoto said. "Do you two mind going outside?" he asked. He figured it would be easier if explanation and comforting were done separately.
Rei nodded and walked outside the room with a lot of difficulty because Nagisa was clinging to him like a koala-baby to its mother. He closed the door behind them.
"I'm sorry about all this, Sakamoto-sensei," Makoto said.
"I should be the one apologizing, although I don't even know what I've done wrong," Sakamoto answered.
Makoto smiled. "You couldn't have known. Nagisa doesn't have a biological family. Sure I am his father, but I have just adopted him and Rei. The two of them aren't even related by blood. Therefore a family tree is a difficult task for him to do," Makoto said.
Sakamoto nodded. "I see," she said. "I feel really bad now… I should have given the class another task," she mumbled while looking down at her hands.
Makoto shook his head. "You didn't know, there is nothing to feel bad about. If you want, I can make him do it for an imaginary family," he said.
Sakamoto shook her head. "It's fine," she said. "He doesn't have to do it. The intention of this was for the kids to learn more about hiragana, and he already knows everything and is very good at it. There's no need," she smiled.
Makoto nodded. "I might just have him do something anyway. He has to learn that he can't skip stuff at school just because he dislikes it,"
They spoke for a short while longer before Makoto gathered Nagisa's things and said goodbye to Sakamoto. He then took both his boys home. Nagisa ended up making a family tree for a penguin family and proved his lack of artistic skills. He showed it to Sakamoto, but never made a presentation for his class. Eventually the entire incident was forgotten, but never did the staff forget that Nagisa was an orphan again. Especially not Sakamoto-sensei.
So, this might not seem too important at the moment, but in the next chapter, you will see why this is actually very important to the plot.
BTW Noticed the kids Ayato and Akito? It's not like they're important unless you ever read the Fairy Tail story, The Titania Twins and the sequel: One Gray or Another. Ayato and Akito are a direct reference to the OC main characters, Aya and Aki Titania. This is nothing important, I just wanted to point out this fact.
That's it for now
Jackie