On a day-to-day level, Leo often meets with her on her apartment rooftop to chat and do some training drills early in the morning when he's out on his own doing some morning exercise and before she has to get ready for work. He volunteered the idea after he learned that she has some hand-to-hand combat experience and she expressed wanting to sharpen her skills again since she's years out of practice with any sort of regulated training. They both enjoy the quiet time together getting to focus fully on the common goal of improving their skills.

They get along very well since they're both dedicated, goal oriented people. She ends up being valuable to the group on certain missions as well because of her skills with firearms and her mindset as an ex-soldier. Her willingness to follow Leo is significant, though, and speaks to her respect for him as a leader because he's actually earned it.

Daphne grew up in an environment where trust and respect were not earned but automatically given to the people barking orders at you. Now removed from that environment, she holds a lot of distrust towards any sort of traditional authority figures (i.e. cops, military figures, politicians, etc). She will not follow someone blindly after a lifetime under Bishop's influence where she was expected to believe whatever he taught her. Her trust is not easily won but Leo proves himself worthy of it over time. She doesn't just respect him as a friend but also as a leader.

Their dynamic shifts though when he finds out about her past and it's only worsened when he goes through his PTSD arc in season 4.

For context: her secret is revealed in the worst possible way to all of the guys when she helps them rescue Splinter in s3ep24 'Bishop's Gambit' and Bishop recognizes her despite her efforts to hide her face.

Leo's reaction is outwardly more subdued compared to his brothers despite how shaken he is at the information. The idea does cross his mind that she might have hidden this from them for a more nefarious reason, but he does his best to give her the benefit of the doubt and remain as neutral as possible. Partly because his brothers have clashing reactions and he's trying to keep frictions from getting worse but he also doesn't want to accuse her of anything. He doesn't want to believe that she'd do this to hurt them (and he's correct about that detail) so he's willing to hear her side of things and try to understand why she lied to them for so long. He doesn't really like her answer but he does understand where she's coming from even if it does bother him deeply that she kept this from them for so long when she knew they had run ins with Bishop.

In the aftermath of finally stopping the Shredder, however, Leo experiences something Daphne has known ever since her last field mission with the EPF: the crushing weight of guilt in knowing you did your best to help/protect others only for it to not be enough. (That whole mission was what led Daphne to start questioning Bishop and the EPF before she escaped as a teenager. I can talk about it more in another post if you're interested. It's also when she got her massive shoulder scar, so Leo getting his scar in Exodus makes them become shoulder injury twins )

The effect this event has on his handling of their friendship is...bad to say the least. Now, since 'Exodus' happens right after 'Bishop's Gambit' (s3 ep24) in canon that means that everyone is still stewing in their feelings regarding the reveal of Daphne's past. It's not good for the group dynamic and it leads to some tensions during the execution of the mission to stop Saki (particularly between her and Raph as well as Raph and Donnie which is part of why Mikey and Raph are put together when sneaking into the tower).

Leo managed to push through his own reservations towards Daphne for the time leading up to 'Exodus' because they have this enormously important mission and need her help, but after everything happens and the dust settles when they're all back at the farmhouse, all of his remaining feelings that he bottled up before start coming to the surface. Daphne sticks around the house with April and Casey to help keep up the place and take care of the guys and Master Splinter but her presence is quickly determined to be more of an issue than an aid (at least at first) so she settles on returning to the city during the week to work and coming up during weekends to help if they ask for her.

Leo snaps more easily around her in particular and she does her best to give him space. With everything that happened, it's natural that Leo begins to reevaluate a lot of things leading up to that final confrontation with the Shredder. He turns it over and over in his mind, trying to figure out what he could have done differently that maybe could have led to a different outcome, an outcome where he and his family didn't need to almost sacrifice themselves.

In the midst of processing all these feelings, he's also questioning his previous decision to be as forgiving as he was towards Daphne. Afterall, he gave Karai the benefit of the doubt and that had ended with him getting stabbed. So it's natural that he'd start to wonder if trusting Daphne is truly a wise decision given that his previous attempt to extend goodwill to someone similar to her nearly cost him his life and his family.

Daphne feels incredibly guilty for lying to all of them but there comes a point where Leo gets so worked up and questions her directly why she lied for so long, whether she actually cares about his family's safety and how she could be so selfish to keep that information to herself when he and his family have a right to know who exactly they invite into their home. It's not undeserved and Daphne knows this, but she's still deeply hurt at his implication that he doesn't trust her not to willingly hurt any of them.

Things are tense and cold between them for a while until they finally get to talk again after he comes back from Japan. She apologizes again for lying and admits he was right about her behavior, that she should have thought about them and their safety over her own feelings and selfish fears, but that she'd like to rebuild their friendship if he's willing to let her try. He agrees and apologizes for the way he spoke to her and they enter a new chapter of their friendship with a stronger foundation and understanding of each other after this conversation.

Raph

Raph's relationship with Daphne is kind of a mixed bag. In some ways they know each other the best of anyone else in the group and in other ways they cannot understand each other to save their lives.

For the most part they tend to get along but when they butt heads, it's cataclysmic.

From a strictly shallow outward perspective, he is most similar to the people, particularly the men, she grew up around at the EPF. So she feels more comfortable around him when they first meet because she feels like she knows how to respond and act around him.

While most of the people around her were her superiors in some way when she was growing up, she did come across more hotheaded younger men who took issue with her when she would speak up or ask questions during combat training drills. The way she earned their respect was by beating them at their own game (or she just incurred more irritation and resentment).

Either way, she knew how to respond to Raph's initial standoffish attitude: by engaging with him in some sort of sparring match, first verbal then eventually physical once she started training again. She met him on his level on his terms, and they quickly warmed up to each other.

They both also have issues with their tempers. Raph's is more expressive than Daphne's and since he's used to openly expressing his feelings, his outbursts are generally more consistent in their degrees of extremity. But Daphne...oh boy. She has a habit of bottling her feelings until she explodes and when she does...just get out of her way.

In this sense, they understand each other extremely well. They rely on each other when they need someone to vent to or just need someone to sit quietly with. As much as they both love Don and Mikey those two can yap for HOURS about certain things and Leo can be a bit more...preachy? solution oriented? when a problem arises. Sometimes Raph and Daphne just need silence and a supportive presence and they find that in each other.

Here's where things get bumpy though.

Everyone has different reactions to Daphne's past and her lying about it but Raph's is the most visceral. He's extremely hurt to learn that a close friend has been lying to him and his family for as long as she has. That hurt, as if often does with him, comes out as anger and in the immediate aftermath of the revelation and her explanation, he wants nothing to do with her.

He avoids her like the plague, refuses to even be in the same room as her if he can help it. She gives him space but the tension only continues to build the longer they go without speaking. When she's at the farmhouse doing what she can to help them recover after the events of 'Exodus', he refuses her help or makes snide remarks when he can't afford to refuse it.

She does her best to brush it off but eventually it gets to be too much when he refers to Bishop as her dad one too many times and she just loses it. They argue a bit before she leaves the house and decides to just stick around on the weekends if April, Mikey or Don call her up.

There's friction between Raph and Don because of this too. Don's hurt over Daphne's lying is not as obvious as Raph's and instead of being distant with her when she finally tells them all the truth, Don chooses to continue spending time with her in an effort to get more of an answer. He knows there's a deeper reason why. He'll sneak out in the evenings to visit her apartment and not return until late at night or sometimes even the next morning. This bothers Raph a lot. He knew about Don's crush on Daphne for a while before everything blew up and he feels like his normally logical levelheaded twin isn't seeing the severity of the situation or if he is, he's choosing Daphne over their family.

It's made all the worse because Raph and Don do not fight often and when they do it's usually resolved fairly easily, hell Don doesn't fight with anyone really. So the fact that Don is not budging on his stance with Daphne when Raph is on the other side of the fence, it not only hurts Raph further but this is fairly new territory for the twins in their own relationship dynamic.

Raph and Daphne eventually do patch things up after they finally air out everything that's been unhealthily building between the two of them (the fight isn't pretty but it's cathartic).

Something I do love about their friendship though: at one point when the two are still on bad terms, the guys have a run in with Bishop who approaches them about helping him retrieve Daphne in exchange for the EPF officially leaving their family alone and before Leo, Mikey or Don can even open their mouth, Raph is the first to defend her. He all but spits in Bishop's face at the suggestion.

I think it's really important to understand that he's really only upset that she lied, not that she was Bishop's kid. Raph knows she didn't have a choice in who raised her and he knows she would never betray them or willingly hurt them. He knows this so intuitively that he's the first to tell her father to fuck off and leave her alone even when he and Daphne are not on speaking terms.

Mikey

Mikey holds the status of "favorite little brother" in Daphne's heart and all privileges that accompany the title. But it is worth noting that said privileges were well earned on his part.

Though he was probably the most upfront and welcoming when she was beginning to integrate into the group, it took her the longest to fully warm up to him because his outgoing friendly personality was a bit too much for her at first. She had very little exposure to extroverted emotionally open people given that she grew up in a military environment and had Bishop (the world's most emotionally constipated man) as a father figure.

As a result, she didn't know how to process Mikey's attempts to get to know her. It took many a movie night for him to crack her exterior. But when he did, there was no going back.

Daphne would kill, fight and die for him.

He's the first person to get her to laugh so hard that she can't breathe. When he finds out that she sketches in her free time, he's ecstatic about it and shows her his own drawings and they bond over their love for creating art.

Bishop had never been very receptive to any of Daphne's more artistic hobbies as a child and discouraged her from pursuing them if he deemed them unimportant or useless to her future career. As a result, she kept her art to herself and became extremely protective of it. She only began to seriously pursue drawing again after she left the EPF and once she found a kindred spirit in Mikey, her skill took off exponentially.

Mikey also figured out that she returned Don's feelings when he saw studies of his brother in her sketchbook. From then on Mikey was kinda relentless in trying push her and Don together.

When everything came out about her past though, Mikey's absence hurt in a very unique way.

Raph and Leo avoiding her, she could expect and understand but knowing that Mikey was hurt enough to stop talking to her for a bit was soul crushing. He was always the most emotionally intelligent of all of them, always knew what to say, always had something to say about pretty much anything. So his silence hit her in a way that Leo's and Raph's didn't.

When it came to his initial reaction though, Mikey did advocate for her. He insisted that she had to have a good reason for choosing to do what she did and while he was definitely more forgiving than Raph or Leo, he couldn't hide how hurt he was.