A/N: There's a deluge of episode tags for the season finale, but I couldn't resist adding my own because my take on Booth's possible reaction seems to be a little different from most of what I've read so far.
The text in italics is the Confiteor, the prayer spoken during the Penitential Rite at the beginning of every Catholic Mass.
I confess to almighty God
and to you, my brothers and sisters,
that I have greatly sinned
He has no idea how long he's been kneeling in the narrow, uncomfortable pew, but it doesn't matter anyway; it's not like he has anywhere else to be at this hour.
His back and legs are beginning to hurt, but he doesn't move. He welcomes the physical discomfort, embraces it; it's easier to bear than the pain that's eating at his insides.
The pain, and the leaden weight of guilt.
He has failed them.
The woman he loves, the child they brought into this world – they're out there somewhere, on the run from a law that should be on their side, that he and she have both dedicated her lives to. They both used to rely on the law being their protection, yet what once was their strongest shield has been turned into a deadly weapon wielded against them by an enemy they couldn't stop – he couldn't stop.
So she did the only thing she could, now that no place that the law's arm can reach is safe for her anymore – but it kills him to know that she had to shoulder the weight of her decision alone, that she had to keep it secret from him because he is the law, because she wasn't going to make him choose between his heart and his sworn duty.
It doesn't console him that she knows he would have chosen her, that he would have spat the law in the face for her sake. They both felt the noose tightening around her, and he knew the moment Max brought it up that the old con was right, that she wouldn't stand a chance once she disappeared into a system that has been perverted into a death trap for her. He knew, and yet he couldn't bring himself to say what needed to be said – and he, who thought he knew her better than anyone else, never suspected that she would hear the words he hadn't spoken.
She knows he'd betray everything he believes in for the sake of his family, and he can't deal with the fact that she decided to spare him that.
in my thoughts and in my words
How often has he told her that he's her gun, that he's the one who'll protect her, who'll take the bullet meant for her, who will die rather than let anything harm her?
And yet she couldn't trust him to keep their daughter safe, had to burden herself with a baby while she's on the run. He clung to the hurt, to the bubbling resentment in his stomach because it was easier to deal with than the empty, deadly weight of despair while he dazedly made his way back home from the church – until he saw Pelant standing in the nursery on the footage from their security cameras, until he was forced to realize that she was right not to entrust him with his daughter because he wouldn't have been able to keep Christine safe either.
Being Bones' protector has been the most natural part of his identity ever since she first called herself his partner – but she's out there now because she has to protect herself, protect her daughter, and has taken it upon herself to protect him as well.
She had to do what he couldn't, and she had to do it alone. He doesn't know what to do with what's left of himself now that she's gone.
in what I have done and in what I have failed to do
He will never forgive himself for walking straight into Pelant's trap. If he had kept a clear head when he got the call, if he had called Bones back immediately, or let Angela trace the call instead of following his panicked instincts, the seething hatred in his gut that was dying to have a go at the creep who kept torturing them – then he wouldn't have let a killer loose on everyone he cares about, wouldn't have cut himself off from all means to catch him before he can harm them further. Pelant handed him the rope to hang himself, and he was only too eager to do him the favor, and now Bones and his daughter are paying the price.
For as long as he has known her, he has tried to teach her to listen to her heart, even though there were moments that made him realize she wouldn't have needed the lessons. She has always been fierce in her fight for what she believes in, and he doesn't know how he's supposed to live with the fact that she's now fighting without him by her side because he failed to learn from her, because he couldn't put his heart in a box when it might have saved them.
She used her cool, ruthless logic – always her sharpest, most trusted weapon – and did what he couldn't, what had to be done no matter how much pain and suffering it would cause them, and she may very well have saved them all by doing so. If the choice had been his, he would have insisted on going with her, but she was right again, he is needed here – he's the only link to the system she has left, and no matter how useless it may seem right now, they'd be nothing more than leaves in the wind if she had let him sever that last precious connection.
He can almost see her making the decision, head overruling heart when it comes to her choices, and yet heart forcing her to make those choices in the first place because she needs to keep her loved ones from harm.
He didn't think he'd ever be glad that Parker is half a word away, but now he's immensely grateful that the boy is back in England with his mother – if he were here, his son would just be one more person Booth loves but can't keep safe, now that his hands are tied and he has eyes watching him wherever he goes.
through my fault, through my own fault
He's back at work, even though he's stuck behind his desk and isn't allowed to go anywhere near the agents who are working Bones' case. He hates the pity and the badly concealed curiosity, but he needs to be there in order to stay in the loop on the investigation against Pelant – not that the FBI is still doing much in that regard since not a shred of evidence in the loony genius murder points to him.
The squints do what they can, and Booth tries to take comfort from that even though he can see what it's costing them, and how little success they're having in their efforts. He visits the lab every day to check on what they have and wonders if the disappointment and reproach he sees in everyone's eyes is real or just his imagination. He knows he has let them all down by failing one of theirs, and he tries to keep their spirits up since there's nothing else he can do to help them. The evening Cam came over to check on him was the only time he allowed himself to break down and cry into her shoulder, but it's a lapse he's determined not to repeat. He sleeps on the couch in the living room because he can't bring himself to set foot in their bedroom, to walk up the stairs towards the empty crib in the nursery, but these things don't matter, he doesn't matter – all that still matters is the job Bones and Christine need him to do.
He could easily tell the FBI everything he knows about Bones' escape because he knows absolutely nothing, and he's torn between being glad that Max will be there to help them and hating that Bones now depends on the man who once abandoned her when his old crimes came back to bite him in the ass. Booth has always respected Max, but he isn't in the mood to be forgiving right now – he's grateful for Max' help, and he knows the old man will watch over his daughter and granddaughter, but he resents Max' all-knowing act because their situations don't compare, because Max and Ruth Keenan ran from the consequences of a criminal past while she has done nothing to deserve this.
through my own most grievous fault
He knows that Bones would berate him for feeling that it would have been his job to protect his family. She would remind him that they're partners, that they have always faced danger together, that she's no damsel in distress who needs her White Knight to swoop in at the eleventh hour. It's what she would say in that stern, no-nonsense teacher voice of hers, and he would readily agree with her, but it doesn't change the feeling that he failed her when it really counted, that he should have been her paladin in this fight instead of the other way around. He once told her that she helps him being a guy because guys fix things, but now she has to deal with a mess that was too much for him to clear up, that he even made worse when he handed the killer who is after them his freedom on a silver platter.
For as long as Booth can remember, he has struggled with the fear that even his best efforts will never be good enough, that in the end, nobody could ever be bothered to stay with him because he doesn't deserve to be loved. It's not quite the same now, because he knows for certain that she loves him, but thinking back to those last moments before she left it hurts to realize that she wasn't certain he knew because she felt the need to reassure him.
He saw her expression when she drove away, and it's like a stab to the heart every time the image surfaces in his memory. She knows what it means to be left behind, to watch your family leave you – and her face told him what it did to her that she was now leaving him to go through the same ordeal.
He isn't sure whether that makes it better or worse.
Therefore I ask blessed Mary ever-Virgin,
all the Angels and Saints,
and you, my brothers and sisters,
to pray for me to the Lord our God.
He'll do everything he can to bring them back safely, but right now he's only too aware of how little he can do, how he's hitting dead ends at every turn, how all his efforts have been in vain so far because he's trying to run a race with chains around his feet and a blindfold over his eyes.
So he prays, head bowed over clenched hands in a dark, empty church, because it's the only thing still in his power to do, but not for himself, never for himself.
All his hopes and prayers rest on God and His saints to do what he couldn't.
Keep them safe.
Bring them home.
A/N: Just to clarify – I didn't write this fic to put blame on Booth. It's just that, given who he is, I would be very surprised if he didn't blame himself after what went down in the finale.