Usagi Yojimbo DojoBoard

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Why would Mariko tell Jotaro that Usagi is his father. Especially after the whole "protect the bond between Kenichi and Jotaro" thing. She even told Usagi to leave to basically protect that secret which she wasn't even going to mention to him until he forced the issue. Mariko and Kenichi for the longest time were the only ones who knew and Kenichi cared enough for Mariko to protect her from the shame of bearing a child out of wedlock. So at least we know they've come to terms with it, but telling Jotaro seemed to be needlessly straining the relationship with Jotaro who didn't know.

I imagine this came as something around the time of Jotaro deciding to train with Katsuichi.

I haven't yet read the TPBs where Usagi and Jotaro travel together, but does Jotaro explicitly mention that it's his mother who told him about the secret ?

Otherwise, Jotaro may have guessed by himself. He's smart enough. Katsuichi noticed similarities between Usagi and Jotaro, and Koji Nakamura too, while the later observed them only two days or three.

Yeah, I think Jotaro figured it out himself.

I'm pretty sure Mariko told Jotaro. However, it was Jotaro's choice not to tell Usagi before they parted, because he feared Usagi would give up the Path to look after him.

Jotaro (to Katsuichi in the story Hokashi part II) wrote:
"... before I left home to study with you mother told me a secret, Usagi is my real father -- but she didn't say if he knows it"

My assumption on reading Fathers and Sons was that Mariko told Jotaro because he wanted to know why she supported him in seeking out Katsuichi rather than going with Kenichi's wishes that he study at the Dogora school

Perhaps it is a timing thing. A samurai, even a shugyosha, deserves to know who his real father is. To hold back such info forever would be dishonorable. Perhaps in the beginning, when Jotaro was much younger, Mariko did not want him to know. Being merely a child, he needed a father at that point, nothing more. Such news would serve to confuse the child. That is why she asked Usagi to leave...not indefinitely, just for a time.

Now Jotaro is older, about 10, and is training to become a samurai. Perhaps the time was right for him to know, at east in the eyes of Mariko.

I agree to that and also think that Jotaro needed to be told - therefore "giving him the choice" but he did not tell Usagi.

But if Jotaro knows...then...does'nt he feel a little uncomfortable that now knowing the fact that Kenichi is'nt his real daddy? How does he feel when he's around Kenichi? Like, does he still think of him as "Dad" or just...a stranger? I could be wrong tho'.

Many children still call their adopted/foster/step father "dad" even after finding their biological father if it's the person they've always grown up with. But I can't say for Jotaro what he will do now.