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Bruce should have said no. He had enough personal problems of his own, with Dick in New York with the Titans and barely speaking to him, and Jason insisting on helping him with the patrol.
He had no time for an eight-year-old half-human, half-Kryptonian clone, and the part that worried him most was the human part, of Lex Luthor, of all people.
It was the second time Luthor had successfully cloned Superman, and Bruce was beginning to doubt that his type wasn't tall, dark, and Martian.
However, despite what some people thought, he recognized his limitations and couldn't handle another kid just now.
But Clark had looked at him with those puppy dog eyes, biting his lip, wringing his hands, saying, "I know I'm asking a lot…" sounding so, so guilty, and Bruce had given in.
Don't judge him, he was just a man, and his friend/date/boyfriend perhaps knew his weaknesses.
That's how he found himself in the kitchen at 3 PM, with an eight-year-old staring at him as he drank apple juice through a straw, and Jason sitting across the table trying to do his homework.
Keyword: trying.
The twelve-year-old was actually waiting for something to happen that would drive Bruce crazy, and his anticipation was rewarded.
"Are you my mother?" the boy suddenly asked, staring more intently at him with those ice-blue eyes.
Bruce froze completely, while Jason barely held back his laughter. Kon, however, noticed and glared at him. "What's funny?"
"Jason isn't making fun of you," Bruce quickly interjected, because having an angry young Kryptonian rampaging in his kitchen was the last thing he wanted. "He's just surprised. What makes you think I... am your mother?"
Perhaps it had to do with the kid lab upbringing. He doubted the scientists had bothered to teach him gender norms before The 101 Deadly Techniques for Killing Your Enemies.
Kon shrugged. “I look just like you. We both have black hair and blue eyes. I like the way you smell. Superman took me to you right after he found me, and you two seem to like each other. You must be my mom.”
“Superman also has black hair and blue eyes,” Jason pointed out to the boy, but Kon retorted, “But he has curls. He and I don’t have curls. So if I take after someone, it must be my mother. Are you my mother? Is that why Superman brought me here?”
“Ah, Kon…”
He was about to contradict the boy as delicately as possible, but the clone continued. “Besides, he said he was taking me to a safe place, and the scientists made me read these books, and there it said mothers keep their pups safe. So, if I'm safe here, it’s because my mother is here.”
His heart stammered. He didn't know what kind of books they'd made Kon read in the lab—probably nothing good, the phrase sounded sweet out of context, but who knows where it came from—but he felt all soft at the realization that Kon felt safe in the manor, even though Bruce was a stranger.
In fact, Bruce felt particularly weak, especially because of the puppy dog eyes the boy was unconsciously giving him.
Kon was practically begging him to say yes, I'm your mother, no one will hurt you again.
He wanted so bad not being alone, someone who understood him.
And as already mentioned, Bruce was a very, very weak man.
"Yes," he coughed, while out of the corner of his eye he saw Jason typing something on his phone, "I'm your mother. If you want me, I..."
He didn't have time to finish before the boy jumped off his chair and literally flew to him, hugging him so tightly he broke his ribs.
Bruce, however, simply grimaced and stroked the boy's head. Sooner or later, they'll explain to him the whole mess that brought him into existence. But he won't ruin the moment, not when Kon was already traumatized.
What harm was there—besides the teasing he'll surely be the victim of—indulging in a childhood fantasy?
Spoiler alert: Apparently, Kryptonians had a crazy reproductive kink, as demonstrated by Jor-El's message to his son. Who knew Clark had one, too, but for Bruce and only him?