Random TL;DR
Because I feel like I need to get a stronger grip and all this is in my head already.
On Shibusen and partnership
So. To start out, Naomi cooperates so much with Shibusen for two reasons.
A) She's a doctor. Especially given her past and her need to atone for it, Naomi feels compelled to treat those who need treatment and that includes the people in the war. While she wasn't one of the direct factors behind GUILT's development (she was sort of in-but-out: she had an idea of what was going on, but she didn't seem too familiar with Kyriaki or Savato themselves in the last Z episode), she was responsible for helping it along to an extent. No matter how many people she treats, it may not make up for all the harm GUILT has already caused. Even after becoming a medical examiner, this compulsion still holds true. It's even how she meets Alyssa--she's busy, but the whole "But you're a doctor, miss. :( Please help the kitty" thing prompts her to give in and help the kitty.
B) About as importantly, Shibusen can give her what she wants. Really, all Naomi wants to do is live a quiet life with her daughter figure...occasionally working with the FBI on murder cases, but besides that. Death City is definitely not the quiet life, but they can return her home if they win. That means helping them win is definitely in her advantage.
C) Shibusen cooperates with her, she cooperates with them. Naomi's been cornered into doing things before. With Delphi it was "We gave you a new life, so you have to do work for us." With Caduceus it was an agreed "I give you material and my atonement, you give me amnesty and my atonement." With the US government it was "We're letting you in our country, so you have to do work for us." With Shibusen it's "We dragged you in here and that's our fault, so you don't need to do anything you don't want to do." Compared to everyone else except maybe Caduceus, they're much nicer than most of the other authorities she's dealt with in the past and being able to work on her own terms feels good.
Now, that doesn't mean Naomi is happy about everything. She's become a surgeon/medical doctor again. It was her choice, but really she considers that part of her life behind her. To a degree she wants it to be behind her. At first in Trauma Team she's hostile to Little Guy's renewed presence in her life because guess what, huge reminder of her past. She can't escape her past (hello deal with the feds to actually be allowed into the US), but it dredges up things that she'd rather not revisit. Naomi's life is a series of moving on from things, taking on new lives--from the surgeon with a broken career to the Delphi agent to the atoning Caduceus surgeon to the dying medical examiner waiting for her life to end (and then the hopefully recovered medical examiner with a little girl to take care of).
Naomi is happiest at the last of these steps! She has a healthy appreciation for life, and there's a sweet little girl to keep her world bright. Before she was content at Caduceus, but there everything was about atonement for what she'd done in the past, and just being a doctor. Post-Trauma Team, for once her life feels open-ended. Returning to duty as a surgeon is a step back, again one of the things she's moved on from. True, she retired from surgery only out of necessity--but being an ME is her life now, and she likes it that way. On the other hand, she knows there's a much higher need for medical treatment on live people than autopsies in Death City (and would rather keep it that way), so she's just sucking up, dealing, and focusing on the fact that one day she'll hopefully get to return.
The fact that she's going back to the surgeon role again, however, does not mean she'll be open about everything else. Naomi's even trying to keep a lid on her Healing Touch, and her ability to hear dead people. They don't matter in SC anyway, with abilities taken away, and usually when things like that get around it ends badly (i.e., in job loss or blown up eight-year-olds). Delphi? Don't even try. Naomi doesn't even intend to tell her partner about any of it.
AND REGARDING THAT. Naomi and partnership. I had some doubts on this for a while, but after asking people who knew Soul Eater and SC partnerships I heard it would work. I believe this is mainly on a basic level--Naomi can form a partnership because:
A) She wants this to work. It's partly proof that yeah, it can work for her, and she's heard that partnerships are important. Having Brock as a weapon is also highly useful because...
B) Her "weapon" is a healing item. I don't think Naomi would ever form a partnership with an offensive weapon, because using one means going out and harming others--possibly even killing. That's not the sort of person she means to be.
This isn't to say she won't harm anyone ever! Just in Naomi's first playable chapter the murderer goes after her and she seems to have no qualms about shooting him in the leg; she also hints that she'd kill him if he tried anything else ("Don't move. I see corpses all day, one more won't bother me."). But that's different in a way, because that would be self-defense against a murderer and, more importantly, her own choice. Going out and fighting for SC, though, would make Naomi feel used. As I mentioned above, she's been used as a tool for others often enough and she hates that. With Brock as a weapon, she's aiding Shibusen and she's returning to a part of life she left behind--but it's on her own terms, which makes a lot of difference.
Buuut back to the original point. I believe Naomi can form a partnership for these reasons; the strength of the partnership is questionable. Right now there are maybe three or four people Naomi really, truly trusts. Alyssa and Little Guy are the most obvious, and Derek Stiles probably counts too. Possibly Chief Wayne, since he's a nice guy. Naomi trusts Brock to be a reliable partner, but she wouldn't really tell him anything personal right up front. I imagine she doesn't even tell Alyssa things like that, at least not for a long time. (Delphi and GUILT-level stuff? Heck, I've got fic on how long that takes.) So as far as Brock goes, she still tries to keep some distance, and I imagine they're going to get a little stalled in growth until that changes. This might change as they work together more, of course, and I'll definitely have fun if she does!
On romance and intimacy
So while I stared at the moving-in log with Brock, I realized something. While Naomi isn't really looking to do the whole romance thing herself, she has pretty relaxed views on intimacy and sex. She seems to have no problem invading Little Guy's personal space to fluster him into doing what she wants, for one, and she seems pretty much unfazed over Abigail Parker and her boss having an affair. And of course, her outfit. I will never understand how Naomi manages to wear what she does, but I assume it's the same reason Hank's partially bare-chested and Tomoe wears her lab coat over a kimono (i.e., the character designers did it). I'm guessing that where strangers are concerned her attitudes toward sex and romance are that while fidelity is the "moral" way to go about it, stuff happens. She's seen worse than cheating spouses. When things get personal (if it happened to a friend, or herself) she'd probably be concerned or hurt, but try and take things rationally so that everyone regrets as little as possible.
As for the chances for her own love life...well, I don't see Naomi actively looking for anyone. Maybe a couple dates when she was younger, but nothing serious--especially since personal headcanon says she moved around a couple times. Furthest it goes, she'll have good chemistry with someone and do some light teasing with a mutual understanding that it isn't serious. (Sorry, Little Guy.) Naomi's not looking for someone to share all her intimate secrets and feeling with. Going with what's in the game it's Alyssa, not Little Guy, that she chooses to open up to most--she's shown a few kuudere tendencies over Little Guy, but it's Alyssa with whom she goes "Oh, lunch? Whoops, I forgot. Here, I'll get you anything you want." Which makes sense in some sense, because she's dedicated herself to giving Alyssa a good life.
Anything further than that...difficult. I like my one-sided Naomi/Little Guy, but personally I'm not sure anything mutual would work. Naomi confides in Little Guy, for sure, but for all the "nice tie" bits and their history I think she sees him as a close friend at best. I actually think their history is the big deterrent--that if Naomi ever decides she likes someone that way, it would be someone to whom she chose to divulge her past. (Which is a total of one person in canon, but hey.) Is this really that important? To me, it is. I see choice as being a big factor in Naomi's life, because much of the time she doesn't get much as covered above.
...Also, any guy she had interest in would ultimately need Alyssa's approval, but it's Alyssa. Not too hard, man.
On Shibusen and partnership
So. To start out, Naomi cooperates so much with Shibusen for two reasons.
A) She's a doctor. Especially given her past and her need to atone for it, Naomi feels compelled to treat those who need treatment and that includes the people in the war. While she wasn't one of the direct factors behind GUILT's development (she was sort of in-but-out: she had an idea of what was going on, but she didn't seem too familiar with Kyriaki or Savato themselves in the last Z episode), she was responsible for helping it along to an extent. No matter how many people she treats, it may not make up for all the harm GUILT has already caused. Even after becoming a medical examiner, this compulsion still holds true. It's even how she meets Alyssa--she's busy, but the whole "But you're a doctor, miss. :( Please help the kitty" thing prompts her to give in and help the kitty.
B) About as importantly, Shibusen can give her what she wants. Really, all Naomi wants to do is live a quiet life with her daughter figure...occasionally working with the FBI on murder cases, but besides that. Death City is definitely not the quiet life, but they can return her home if they win. That means helping them win is definitely in her advantage.
C) Shibusen cooperates with her, she cooperates with them. Naomi's been cornered into doing things before. With Delphi it was "We gave you a new life, so you have to do work for us." With Caduceus it was an agreed "I give you material and my atonement, you give me amnesty and my atonement." With the US government it was "We're letting you in our country, so you have to do work for us." With Shibusen it's "We dragged you in here and that's our fault, so you don't need to do anything you don't want to do." Compared to everyone else except maybe Caduceus, they're much nicer than most of the other authorities she's dealt with in the past and being able to work on her own terms feels good.
Now, that doesn't mean Naomi is happy about everything. She's become a surgeon/medical doctor again. It was her choice, but really she considers that part of her life behind her. To a degree she wants it to be behind her. At first in Trauma Team she's hostile to Little Guy's renewed presence in her life because guess what, huge reminder of her past. She can't escape her past (hello deal with the feds to actually be allowed into the US), but it dredges up things that she'd rather not revisit. Naomi's life is a series of moving on from things, taking on new lives--from the surgeon with a broken career to the Delphi agent to the atoning Caduceus surgeon to the dying medical examiner waiting for her life to end (and then the hopefully recovered medical examiner with a little girl to take care of).
Naomi is happiest at the last of these steps! She has a healthy appreciation for life, and there's a sweet little girl to keep her world bright. Before she was content at Caduceus, but there everything was about atonement for what she'd done in the past, and just being a doctor. Post-Trauma Team, for once her life feels open-ended. Returning to duty as a surgeon is a step back, again one of the things she's moved on from. True, she retired from surgery only out of necessity--but being an ME is her life now, and she likes it that way. On the other hand, she knows there's a much higher need for medical treatment on live people than autopsies in Death City (and would rather keep it that way), so she's just sucking up, dealing, and focusing on the fact that one day she'll hopefully get to return.
The fact that she's going back to the surgeon role again, however, does not mean she'll be open about everything else. Naomi's even trying to keep a lid on her Healing Touch, and her ability to hear dead people. They don't matter in SC anyway, with abilities taken away, and usually when things like that get around it ends badly (i.e., in job loss or blown up eight-year-olds). Delphi? Don't even try. Naomi doesn't even intend to tell her partner about any of it.
AND REGARDING THAT. Naomi and partnership. I had some doubts on this for a while, but after asking people who knew Soul Eater and SC partnerships I heard it would work. I believe this is mainly on a basic level--Naomi can form a partnership because:
A) She wants this to work. It's partly proof that yeah, it can work for her, and she's heard that partnerships are important. Having Brock as a weapon is also highly useful because...
B) Her "weapon" is a healing item. I don't think Naomi would ever form a partnership with an offensive weapon, because using one means going out and harming others--possibly even killing. That's not the sort of person she means to be.
This isn't to say she won't harm anyone ever! Just in Naomi's first playable chapter the murderer goes after her and she seems to have no qualms about shooting him in the leg; she also hints that she'd kill him if he tried anything else ("Don't move. I see corpses all day, one more won't bother me."). But that's different in a way, because that would be self-defense against a murderer and, more importantly, her own choice. Going out and fighting for SC, though, would make Naomi feel used. As I mentioned above, she's been used as a tool for others often enough and she hates that. With Brock as a weapon, she's aiding Shibusen and she's returning to a part of life she left behind--but it's on her own terms, which makes a lot of difference.
Buuut back to the original point. I believe Naomi can form a partnership for these reasons; the strength of the partnership is questionable. Right now there are maybe three or four people Naomi really, truly trusts. Alyssa and Little Guy are the most obvious, and Derek Stiles probably counts too. Possibly Chief Wayne, since he's a nice guy. Naomi trusts Brock to be a reliable partner, but she wouldn't really tell him anything personal right up front. I imagine she doesn't even tell Alyssa things like that, at least not for a long time. (Delphi and GUILT-level stuff? Heck, I've got fic on how long that takes.) So as far as Brock goes, she still tries to keep some distance, and I imagine they're going to get a little stalled in growth until that changes. This might change as they work together more, of course, and I'll definitely have fun if she does!
On romance and intimacy
So while I stared at the moving-in log with Brock, I realized something. While Naomi isn't really looking to do the whole romance thing herself, she has pretty relaxed views on intimacy and sex. She seems to have no problem invading Little Guy's personal space to fluster him into doing what she wants, for one, and she seems pretty much unfazed over Abigail Parker and her boss having an affair. And of course, her outfit. I will never understand how Naomi manages to wear what she does, but I assume it's the same reason Hank's partially bare-chested and Tomoe wears her lab coat over a kimono (i.e., the character designers did it). I'm guessing that where strangers are concerned her attitudes toward sex and romance are that while fidelity is the "moral" way to go about it, stuff happens. She's seen worse than cheating spouses. When things get personal (if it happened to a friend, or herself) she'd probably be concerned or hurt, but try and take things rationally so that everyone regrets as little as possible.
As for the chances for her own love life...well, I don't see Naomi actively looking for anyone. Maybe a couple dates when she was younger, but nothing serious--especially since personal headcanon says she moved around a couple times. Furthest it goes, she'll have good chemistry with someone and do some light teasing with a mutual understanding that it isn't serious. (Sorry, Little Guy.) Naomi's not looking for someone to share all her intimate secrets and feeling with. Going with what's in the game it's Alyssa, not Little Guy, that she chooses to open up to most--she's shown a few kuudere tendencies over Little Guy, but it's Alyssa with whom she goes "Oh, lunch? Whoops, I forgot. Here, I'll get you anything you want." Which makes sense in some sense, because she's dedicated herself to giving Alyssa a good life.
Anything further than that...difficult. I like my one-sided Naomi/Little Guy, but personally I'm not sure anything mutual would work. Naomi confides in Little Guy, for sure, but for all the "nice tie" bits and their history I think she sees him as a close friend at best. I actually think their history is the big deterrent--that if Naomi ever decides she likes someone that way, it would be someone to whom she chose to divulge her past. (Which is a total of one person in canon, but hey.) Is this really that important? To me, it is. I see choice as being a big factor in Naomi's life, because much of the time she doesn't get much as covered above.
...Also, any guy she had interest in would ultimately need Alyssa's approval, but it's Alyssa. Not too hard, man.