So for this, everything about what I said in the Fem!Castle story is the same as far as Castle is concerned, but Kate is just a normal woman (at first). My original imagining of Fem!Castle looking the same as Canon!Castle, but secretly being a woman is changing to have her features be slightly less broad and softer, the voice being deep and gravelly but still having a slight feminine tinge to it that most people can't hear; she still tapes her breasts to make her seem more barrel chested and masculine, but Kate as a trained and observant detective realizes that something is off about this man Richard Castle. Before questioning "him" she learns about Alexis and Martha, and again, something seems off. She calls up FBI Agent Will Sorensen (who broke up with her to move on, something they both knew would happen eventually, but she got a favor out of him for it) and asks him to look into the alias Richard Castle to link with their real name, using Martha Rodgers as a point of interest.
Will gets back to her the next morning with shocking news: a woman named Erica Alexandria Rodgers. Kate heads over to confront her and meets Alexis and Martha officially, and gets the story about Erica not being taken seriously before she created the Richard Castle alias. She also gets the story behind Alexis and how she came to be (also note that I'm using the Erica being Kate's age backstory, where Erica first got published at 15 and she got pregnant in college from a CIA agent that she doesn't know his real name while getting research for her first Derek Storm novel). It comes out in that conversation that both of them are bisexual, which is something Kate didn't mean to say but she was surprised when Erica said it that she just blurts out "you too?". It should be noted that Erica was that way before she started having to sign women's chests, so that was just a perk. Erica never married, though, and Alexis isn't generally known to be Richard Castle's child; Erica actually does go out in public as herself normally and especially where her daughter is concerned.
Erica runs the idea of making a character out of her for her next book and asks if she can shadow her for a while to get all the gritty details of detective work. Kate is shocked at first, but then everything that happened since she first questioned Erica flitted through her head, and she started thinking "why not?". So she agrees and says she'll bring it up with Roy after this case. They get back to it, find the obsessed fan, but Erica strongly disagrees from the beginning that it's him, showing how the crime scenes are imperfect compared with how she wrote them, and Kate agrees, so they go digging and find the connection to Tisdale. They solve the case and Castle reveals herself to the others on the team so that she can be herself instead of the persona of the man Richard Castle. Fortunately this case was kept low key, and no mention of Richard Castle helping with the case was made, so when Erica Rodgers starts consulting at the precinct, very few people comment, having seen civilian consultants from time to time. Their second case together is similar to how I outlined in the Superpower story I mentioned, including how the two of them gained their powers.
Now for what brought the two ideas together: when Kate comes to the Loft to see if anything strange was happening to Erica, she gets the thought of what the man Richard Castle would look like, and shapeshifts into him and all his parts. Only, when she does it, she also materializes the clothes she thought of his, which appear under the clothes she's already wearing (think Mystique and how she forms the clothes she wears). Erica is stunned, and Kate changes back and excuses herself to Erica's bedroom, where she sheds her clothes and uses her power to form the same clothes on herself. Later, after Erica gets a handle on her power, explaining what it's like and forming the tunnel between the two, Kate takes hold of Erica's shoulder and gets an idea to shapeshift her into the actual Richard Castle, and that causes some discomfort since there's something weird in her panties that she feels doesn't belong. After getting confirmation that she can change other people, Kate changes Erica back.
Things start progressing much faster in regards to their relationship, since they now have a direct line that seems to have almost limitless range between them, their shared thoughts and feelings keep them honest with each other in such a way that they start moving towards a relationship much faster. It soon becomes apparent that they have no problem with this, especially in regards to a physical relationship since Kate now has the ability to give herself male parts whenever she wants (and at times it becomes a bit of naughty fun for them when she decides to give herself such while in public and she's still dressed as a woman otherwise). Let it be said that they don't use protection, because neither of them think that the parts actual work as intended, which is why it's such a surprise when Erica becomes pregnant and she can prove that Kate is the only one she's been with since they met. They will never officially marry, but they do arrange things legally to give each other power of attorney over their affairs and square away everything they would need to in that regard, and they will have more than just the one child, though they will start using protection once the new baby is born (and since Alexis is only 10 at the start of the story, the age gap isn't quite as striking). Also, since they get started early, they wind up having more children than you would otherwise think possible.
As to how everything else, including the case of Johanna Beckett, gets solved, well, that's for another time... I think I'm out of ideas at the moment, other than toying with the thought of having it reversed a time or two so Kate can carry and birth a child as well, though when that would happen, I don't know... Just a thought for later, I guess. I might have the two of them come out about their powers to the rest of the team after Erica winds up pregnant, if only so that it doesn't get too weird to them about them suddenly having a child together. Gates would be a hard sell, but it's possible...
Anyways, I'm done for now. That was a lot, but I did have to combine two ideas together to get it, and it's got some pretty strange stuff in it, so I had to really give it some thought.