AU at the end of season 2, where Mac's dad wasn't who he was revealed to be on the show, but rather an operative with another agency. Everything else is pretty much the same, including the person who laid the clues for Mac to find him.

This chapter is mostly setup for the main story itself, so warnings have yet to really apply, but be aware that Mac's dad is not a positive force in his life in this fic. I will provide specific warnings on individual chapters.

(Title from Sleeping At Last's song 'Three'. Crossposted on AO3.)

James MacGyver has inscrutable eyes.

The first thing Jack observes about his partner's long-absent father is that his eyes are completely empty. There's nothing in them to read or evaluate, no joy, no coldness, nothing to give him an indication about what sort of man James is. Jack has seen this type of look before, on undercover agents, people who have deliberately stripped their own personalities to facilitate integration into anywhere. He's seen it on himself, after too long under, worked hard to make it go away. James' eyes, they're spy eyes, and from the moment Jack meets him, he doesn't trust him.

When he'd thought about Mac's father, about what it would feel like when they finally found him, Jack had always known it would be hard to watch. He's got too much anger for James, the way he'd left his son for all intents and purposes an orphan at twelve, to be at all comfortable with the idea of that man being around Mac again. But it was something Mac obviously wanted, had worked for, obsessed about, hurt over for so long, and Jack can't be the one to try and take that away from him.

So he'd helped. Against his own reservations about what sort of man they would find when they eventually tracked him down, Jack helped. The alternative was leaving Mac to deal with this on his own, and well, that was never really an option.

The day they find him, the day he watches James hold Mac by the shoulders, studying his face like he'd never seen it before - and likely hadn't not as an adult, not in person or up close - Jack makes a quiet vow. He promises himself and Mac that he's going to stay out of it, he's going to keep his mouth shut and his words respectful when he does speak. Whatever his opinion, he can't afford to let his own protective misgivings, his misguided paternal claim to Mac get in the way of the kid building a relationship with his father. If he does, if Jack gives in to the urge to pull Mac aside, tell him he's got a terrible feeling about this and they need to get as far away from James as possible, whirl on James and read him the riot act on exactly what Jack thought of his behavior towards his son, well. Then he runs the risk of losing Mac entirely, and that's not an outcome he can live with.

"Dad," Mac says when he leads the man over, the word sounding foreign and uncertain in his mouth, "this is Jack. My partner with the Phoenix Foundation."

"Jack Dalton," Jack says, smiling politely and holding out his hand. James shakes it, brief and brisk with an offering of his own name, before turning back, pulling his son away with him again, to speak privately.

Mac looks over his shoulder for a moment, gaze anxious and seeking when it locks onto Jack's. Against his numerous misgivings, against every reservation and screaming instinct in his body, Jack forces his smile to remain, and nods. It's a permission, an encouragement. Go, that nod said. Get to know your old man. He hopes he won't regret it.

The three of them stand in that courtyard for what feels like ages, though Jack isn't entirely sure how long it actually is, Mac and James maybe thirty, forty feet away from where he waits in the shadow of a well-cultivated tree. A building looms behind them, the physical spectre of the organization Mac's father has been revealed to work for, one that runs parallel to but separate from the Phoenix. They are aware of one another only insofar as they have to be, communicating only at the highest levels, where it seems James has positioned himself just shy of director. An operative just like them, a thought that leaves Jack with an odd feeling and more questions now than he has answers.

If he'd been here in California the whole time, undoubtedly aware of Mac's presence at the Foundation, why had he not reached out? What had kept him away for so long, leaving his only child to wonder if he was even still alive? That absence, bits and pieces of it coming out over the years, how James hadn't even shown up for Mac's grandfather's funeral, it had done so much damage. Jack is hard-pressed to imagine an excuse that would cover the extent of what that abandonment had done to Mac, the scars it left him with.

Some of his questions get answers when Mac sits in his apartment later that evening, an untouched beer sitting open on the side table next to him, restless fingers picking at the hem of his shirt. Jack is dying to ask, to demand to know what James' reasons had been, what possibly could have motivated him to disappear on his child's twelfth birthday never to be seen again, but in the refrain of the day, he holds it in. Restrains himself. Reminds himself that however hard it is for him to watch Mac caught in this situation, this unbalanced culmination of a long, painful story, it's unfathomably harder for Mac himself, and his role here is support.

His role here is whatever Mac needs it to be.

"He said it was to protect me," Mac says eventually. A thread has come loose from his shirt and he's pulling at it absently, a thin line visible on his thumb where the pressure of the thread marks his skin. He's twisting it hard. "That he left. He said he was going through a lot, and his work was too dangerous to keep doing it and be a single parent at the same time."

"Uh-huh." Nice and neutral, no hint of how Jack feels about that, the immediate instinct to point out 'if it came down to this job or you, it'd be you without a thought'. There's clearly more that Mac isn't saying, and Jack certainly isn't going to encourage him to open up by immediately poking holes in Mac's happy ending.

When he does continue, Jack sees that the happy ending didn't need holes poked in it. At least from where he's standing, the thing is already patchy as hell, because what Mac says next makes his breath catch in his throat.

"He also said he… That it made him angry. To look at me. Because I look too much like my mom, and I…" Not usually one for trailing off, leaving ideas of any sort half finished or unexplored, Mac's voice dwindles down into nothing, conflictedness in every line of his face. "It hurt too bad, to see me, after she died."

"That wasn't your fault," Jack can't help but interject, and when Mac glances over at him, it's with a small smile. Barely a quirk of the side of his mouth, eyes soft, but it's a smile nonetheless.

"I know," he says. "He said so too, that it couldn't be helped," Jack doesn't think he'd go that far, but that's not a hair to split right now, "and it was nobody's fault," Again, Jack is gonna silently call bullshit on that one, "it's just… How things were. He said he regrets it, and he wants to do better. Wants us to do better. He said he wants to have a real relationship with me." There's something like awe in Mac's voice now, like he can't believe what he's saying. Like he can't believe that it's happening for real and not just some repeated dream from a lost, bereft childhood.

"So what are you going to do?" Jack keeps his voice neutral when he asks the question, betraying nothing as to what he hopes the answer will be. And he does hope. He wants to hear Mac say he'll be careful, that he'll keep his distance, take what James says with a fistfull of salt and the wits of a trained operative. That he'll take to heart what Riley hadn't, when Jack had been standing here having this conversation with another child of his heart about another poor excuse for a man who'd never done a thing to earn the title of 'father'. If he's left you before, he'll do it again.

But Mac just shakes his head, looking at the ground, the wall, his hands. Anywhere but at Jack.

"I'm gonna try it," he says eventually. "I'm going to see how it goes. He seemed sincere when he apologized, I mean…" The shrug is an awkward movement, out of place on a person of Mac's skill level, competence in the world, a stark reminder of how young he is, the uncertainty he carries under a confident veneer. How that uncertainty got there. "What have I got to lose, right?"

That's what I'm afraid of, Jack doesn't say. Finding out.

So the next day Mac meets his father for coffee, and the next day for dinner, and for a while, everything seems like it's going okay. Jack misses his partner, aches a bit over the lost time spent together, evenings of movies and weird games on Mac's back porch replaced by working on his car or running on the coast. It's only natural, though, he supposes, for the kid to want to spend quality time with his dad. It's been years, more than a decade, and that leaves a lot of catching up to do.

On top of that, James' organization operates even more in the covert area of things than the Phoenix does, and he's asked for Mac's help with an assignment, a task that would hopefully help them bond and foster trust. It's only natural that, while they still see him at the office, it's become less common for Jack and Riley to encounter Mac when they were off the clock. Even Bozer has reported seeing less of him, commenting around the third week of James' presence that Mac seems like he's hardly been home lately.

It's this same week that Riley corners Jack, and says to him, "That man is bad news."

The assertion comes apropos of nothing, and with a sinking feeling he knows exactly who she's talking about, Jack makes a wordless gesture for her to go on.

"Mac's dad. I have a really, really bad feeling about the guy and I know you do too." It's unusually blunt and unedited, even for her. "I think that if we don't do something, Mac is going to end up hurt."

"Where is this coming from?" Jack asks. "What happened, did he say something to you?"

"What, Mac? Say something negative about his dad, who he's got to know we have doubts about? No, of course not. But I was over at his and Bozer's house today when James dropped him off and I… It's gonna sound crazy but I don't like the way he looks at Mac. Everything about him puts me on edge." Riley must read something in Jack's face, because she turns partially away, arms folding defensively. "I know what you're thinking, and this isn't about Elwood."

Okay, yeah, maybe Jack had been thinking it. "Your dad up and screwed off again after promising he was really back for good this time and now you're scared the same thing's about to happen to Mac. The thought had crossed my mind."

"It's not about Elwood," Riley repeats, voice hard. "It's been months, and I'm not saying I'm over it, but- It's not about him. It's about Mac, and hisdad, and this awful feeling I have that something bad is going to happen."

"You said it yourself, he already knows we have doubts about the guy. If he's worried about getting an 'I told you so', he's never gonna come to us if something does happen. You know how he is, he'd get it in his head we'd think it was his fault and never breathe a word. We have to let him make his own choices." Jack doesn't express the other part of what's holding him back, comments about helicopter parenting circling around his head. How he's afraid that if he oversteps and acts like the father he feels like but obviously isn't now that the real deal is back in town, Mac will feel like Jack is trying to control him and finally pull away so far they'll never get him back.

Riley seems to accept the first part on its own, though, which is a relief. The second bit is not a thought process Jack is keen on sharing with anyone.

"I know. That's why I'm here talking to you instead of him. I just…" The unfinished words sound as strange coming from her as they had from Mac. Neither of them are built with personalities prone to letting things go without seeing them through. "It's not about Elwood, but I know what he's going through, and it sucks, and I don't want it to end for him like- I'm an only child. I've always been an only child. Mac is like my brother. My brother. I don't want to see him get hurt, not if there was something I could do to stop it."

When he puts his hand on her shoulder, Jack can feel that Riley is shaking, just a little.

"It's gonna be okay. And if it's not, we'll put a stop to it. He's not alone, we've all got his back, and he knows it. Alright?" There's a confidence Jack doesn't feel, embedded into the words, and Riley stares at him hard, eyes narrowed and arms still folded. She's scrutinizing him, looking for any indication that she should keep pushing, insist they do something now, before it gets to 'not okay'.

Jack almost hopes she does, just so that he has an excuse to intervene, to stop Mac and repeat Riley's worries to him, worries that have been festering in his own mind since they finally tracked the guy down. This isn't a good idea, this guy is bad news, I have a feeling you're just going to end up hurt again.

"I hope you're right," is all Riley says after a long pause, shaking her head and looking away.

Jack feels a little ill. For all of their sakes, for Mac's sake, he hopes he is too. Even if, in his heart and in his gut, he hadn't truly believed a word of it.