I like to think that at some point over Voyager’s journey, Kathryn Janeway volunteered to babysit Naomi Wildman while Samantha was on shore leave. Partly out of a desire to give her crew some much needed R&R, partly out of genuine affection for Naomi, and partly out of a good old-fashioned “I always thought about having kids someday and I’ve owned dogs and managed ensigns, how hard could it be?” hubris on the captain’s part.
I also like to think this is well into Naomi’s “Captain’s Assistant” fixation, so when she’s informed she’ll be spending a couple of days with Captain Janeway, she sees this as an Opportunity.
Between Naomi’s desire to be a perfect child and thus obviously excellent assistant, and Janeway skimming a few child development papers and walking away with “talk to her like an adult, got it”, both of them are convinced it will be just fine.
And by both of their accounts, it was. Just a small issue with the replicator but that’s fine because everybody likes ice cream for dinner once in a while. Naomi was a Delight To Have Around, and Naomi is returned to Samantha after sharply saluting the captain and then hugging her, which makes Janeway laugh and say “at ease” while also being a bit weepy.
But then a few days later, Sam starts getting odd reports. Neelix says that the first time they re-entered Naomi’s Flotter program, Treevis held Neelix at wooden sword point before kneeling and swearing fealty to Naomi. Naomi just grinned and said “Captain Janeway reprogrammed him to be like a knight so I could learn the responsibility of caring for other people who depend on me! Did you know her mom WROTE FLOTTER???”
Harry approaches Sam the next day asking if everything’s alright because Naomi came up to him and asked whether he “felt a kind of camaraderie - no that was HER word, Samantha - with her over being the two survivors of a doomed alternate timeline”. And then she patted his arm and assured him that “everything would be alright, ensign.”
Most grievously, the Doctor demands to know what kind of media Naomi’s been consuming because she asked him during her check-up if the rendition of Pierrot he’s been humming weren’t “a bit derivative of Jean-Gaspard Deburau, and wouldn’t he like to put his own spin on it?”
Samantha has absolutely no idea how to broach this with the captain, whose comments about Naomi being “extremely bright and interested in philosophy and the arts” are starting to make a great deal more sense.