J/C is canon in Prodigy, as we all already know, but because there is nothing being overtly said or done between the two, there’s always been some gray area for people to say we’re seeing things or reading too much into nothing.
But I can prove it. I can definitively prove they are canon and have been in an established relationship for quite some time.
It all comes down to Isabo’s shirt.
In Isabo's Shirt, she gives him a Bonding Box which she misinterprets to be about friendship and instead accidentally declares her love for him. He, keeping in the tradition of the Bonding Box, then makes her a gift that would symbolize the same: the Mirror. At the end of the story, she returns the mirror and he returns the box. She says "I can't accept this, not yet." The reason she can't accept it is because they both now fully understand what accepting those gifts means: that they are accepting each other's love.
So it would stand to reason that once they do accept these gifts, they accept the love that comes with it.
Janeway not only has the mirror, it is kept on a shelf with her most prized possessions: her Voyager combadge, Chakotay's stone, etc. When she comes into her office/room in the midst of the mission to find him, thinking about Chakotay so deeply, she first touches that mirror and then his stone. That solidifies that that is, in fact, the mirror from Isabo's Shirt. In that moment, she wouldn't have touched something that didn't mean anything about Chakotay, especially when her next move is to take the stone and put it to her heart.
In order to even have that mirror, he would have had to have given it to her, and it can be reasoned that she likely also gave him the box as well. But she has the mirror. Which means she accepted the love that came with it. And this had to have happened BEFORE he left on his mission or he couldn't have given it to her.
This right here proves that they are already in an established relationship before the mission, and Janeway isn't just searching for her friend. She is searching for her love.
And before anyone starts with: "but they never said that was the Mirror from Isabo's Shirt. That could have just been a mirror." Just really think about that for a minute:
In her ready room, quarters, and even in flashbacks back home, she never had a mirror. We always see the items that mean things to her: books, tea cups, statues. But never that mirror. She never even had a wall mirror aside from the one in her bathroom. Someone like Janeway who doesn't really place high value on her looks in that way wouldn't really have a reason to own a small mirror unless it meant something.
And THIS mirror has to be special. It is on the shelf of things that mean the most to her. She would only have a mirror on that shelf if it were that particular mirror.
Also one of the writers/producers of Prodigy acknowledged what the mirror is. This is an Animated show. In animation, EVERYTHING is Deliberate.
So yeah. They're not only canon, they have been established for some time before Prodigy even begins.
(This is what I choose to use my brain cells on, btw, and I'm not mad about it).
