Author's Notes:

Shaking things up, putting the notes up here…

The bonus for this chapter is a plot bunny generated by a question in the reviews… the Commander explains his refusal to just get rid of Storm Shadow. This would have taken place right before Destro successfully impressed upon Storm Shadow that he was not to kill the blond Joes in chapter 30.

Chapter 31

It feels like my head is fighting with itself.

There are a lot of things I don't understand, and I always have trouble remembering anything, but no effort at remembering something, no amount of puzzlement over what's going on, compares to this; I can't understand my own thoughts. Even the very fact that I care is unexplainable to me. I usually don't mind being confused – it's pretty much the norm, really. But this kind of confusion, with all these thoughts popping up in my head, contradicting one another and not making any kind of sense, is dizzying.

One set of thoughts is insisting that Billy is not safe here because we haven't redeemed ourselves yet, we haven't proven that we're not under the control of the Order. Those thoughts are convinced the Commander is going to execute Billy. I have no clue what the Order is, I can't imagine why anyone would think I'm under the control of anyone but my master, and I can't understand why I'm concerned for the kid or why I even remember his name.

Another set of thoughts keeps correcting those first ones, and insisting the Commander is more likely to brainwash Billy than to kill him. Those thoughts also very firmly believe that my master is my enemy and that there is no Order… I can't really form an opinion on that last piece, seeing those thoughts also fail to clarify what the Order is supposed to be, but I'm horrified at the fact there's a part of my head that thinks my master is my enemy.

Meanwhile, a last set of thoughts - that at least feel like my own - is obsessing over how the pain started when the Commander pressed the button on that little remote control he had, right after he said something – what, I don't know – was bad. I think the Commander caused the pain by pressing that button. I certainly did deserve to be punished for making him angry, but that much pain… I think it means that he hates me. Whatever it is I've done, he hates me for it. The realization hurts a lot more than the device he used did.

The set of thoughts that thinks Billy will be executed protests that the Commander would not hurt me even if I displeased him because he's too smart to risk driving me away as long as I'm useful to him and therefore, to his cause.

The set of thoughts that seems to hate my master protests and insists the Commander would hurt me for fun and has been doing just that, and that he'll turn my apprentice into a helpless slave as well.

Disturbingly, the other two sets of thoughts don't argue about the idea that the child is my apprentice, and from there, things only get more confusing as the three sides continue to argue about what is actually going on.

By the time I wake up, the confusion is gone but I'm still not exactly rational: I'm scared out of my wits for Billy. I don't know what happened to cost him his leg and his eye, but I do know what WILL happen to him if he doesn't escape. I'm completely paralysed this time, but my senses are intact, as usual, and I can easily tell Billy is not in the room.

Mindbender, however, is already behind me and the Commander is sitting a few steps away, in a chair brought in especially for him. He puts down the file he had been reading when Mindbender lets him know that I'm awake and walks up to me, glaring.

I know the logical thing to do would be to calm down and just ask nicely; as nicely as I can considering who I'm talking to, anyway. I try, and I fail miserably. I only manage to keep myself from screaming.

"Where is he?" I growl. "What are you going to do to him?"

"MY son will be just fine," he hisses. "I'm having him fit with a prosthetic leg, and he won't even know the difference. You should know, you've never been bothered by the repairs to your spine and that was done with the same technology. The troopers who were good enough to be worth such care in the past have had zero recovery time as well."

My eyes widen briefly – my spine having been repaired by some of Cobra's ultra-modern medical care does explain why my legs were perfectly fine again after a shot in my back completely cut contact between them and my central nervous system.

"Once that's done and once he's done with you, Mindbender will start working on Billy… he and I will be a family again, finally. You've delayed things quite a bit when you broke him out."

"Monster," I snarl. I know I'm wasting my time but I can't help myself. "He's your SON!"

He snorts. "Better a monster than a monster's lap dog," he hisses. "Mindbdender, start. And if he recognizes him again…"

The last thing I hear is Mindbender impatiently saying that I won't before the pain starts, drowning everything.

I report to the Commander's office as usual when I wake up. I knock on the door, dreading how he'll react – I remember how angry he's been for the past couple of days, but I don't remember why and I have no idea whether I'm forgiven or not.

"Come in," he hisses.

I let myself in, close the door behind me and kneel, waiting for my instructions.

"Get up," he snaps. "I want you to meet my son."

"Your… son, Master?"

I could hit myself right now. How could I forget my Master's child?

"Yes," he hisses.

He gets up and motions me to come along. I fall into step behind him and follow him through several hallways until he finally enters a room in the hospital section of the fortress.

The room only has one occupant: a teenager sporting a pirate-like patch on his right eye, lying in bed with restraints preventing any movement below the neck. He turns his head towards us when we enter and his free eye widens.

"My son, Billy," the Commander hisses, pointing to him. "Say hello, son. Don't be shy."

The boy looks straight at me, looking deadly serious. His accelerated heartbeat is the only thing that betrays he's not as calm as he's trying to look.

"Sensei," he says, "you know me. You trained me. You don't belong here, you're being manipulated."

I raise an eyebrow at him. "You have me confused with someone else."

He loses all trace of calm: his pulse shoots up and he starts pulling at his restraints, with no result. "NO!" he yells. "Sensei, you can't…! ARGH!" He turns to his father, looking downright murderous. "I HATE you. You…!"

He stops when I put the point of my sword on his throat. Son or not, talking to my master like this is NOT acceptable.

"You will apologize," I growl. "Now."

"At ease, Storm Shadow," the Commander says. "We have some disagreements, but we're working on them. You are not to react to his behaviour towards me, unless there's a clear and immediate threat."

"Yes, Master."

I sheathe my sword again and step away from the boy. He gives me a look that gives a new meaning to puppy dog eyes before heaving a sigh and turning away from both me and his father.

For reasons I can't fathom, the Commander laughs out loud and heads for the door, motioning me to follow. I bow to the boy on the way out, but I don't think he notices.

The Commander dismisses me as soon as we're back in his office, and orders me to the gym until dinner, citing my latest defeat to Snake Eyes.

Hiding the sting his words cause me, I bow and take my leave.

I'm going through katas when I hear it. It's barely audible, even for me, but it's more than enough: screams of terror, interspersed with pleas and calls for help addressed to the screamer's sensei.

I had already forgotten "meeting" him this morning, but his screams cut right through the fog in my head: there's no confusion this time, I go straight from feeling miserable because I keep failing my master by losing to Snake Eyes to wanting to slowly strangle the life out of said 'master'. Overriding that particular wish, though, is the more immediate need to get Billy away from here.

I run out of the gym, resisting the urge to draw a weapon so the troops won't think I'm about to attack someone and merely assume that I've suddenly decided to run around for no good reason. They HAVE seen more bizarre from me.

I take out a slip of paper and a pen once I get to the hallway leading into Mindbender's lab – it's as empty as usual, so there is nobody to notice I'm actually writing real words. I stop long enough to hurriedly scribble a note to Billy. I intend to yell his instructions at him too, but the note is a backup in case he's still too out of it to hear what I'm going to say and a way to convey a bit of information to Snake Eyes.

LEAVE ME. You can't carry me and still escape. Tell Snake Eyes that Zartan killed the Hard Master, Scrap Iron the Soft Master. GO!

I start running again and tie the note to a throwing knife, ready that knife and two more in my right hand and three other in my left hand: I will need every fraction of second I can save once Mindbender and the Commander realize what I'm doing. With any luck, they're too busy with Billy to be monitoring me right now, but as soon as I crash in, they'll have the option to activate the safety switch and knock me out. I need to make sure Billy is free and gets my message before that happens.

I'd love to be able to simply throw knifes in their throats and kill them there and then, despite the fact it would be a much, much quicker death than I want for them, but I know the safety on the chip will activate by itself if I make a move against the Commander, and I'm pretty sure Mindbender has extended that protection to himself, too. Therefore, I can't attack them – the only thing I can do is make sure Billy is able to dash out of there. I really hope the Commander wasn't bragging on how good a prosthetic leg he's given him.

Billy is still screaming, but there are no longer any words mixed in. From his position in the room, I know he's in the chair, and I can also hear Mindbender behind him. The Commander is standing in a corner, his pulse betraying more impatience and excitement than anything else. I curse inwardly and forcibly remind myself I can't touch him. Although I wouldn't have thought it possible to hate the Commander more than I already did, I certainly do now that he's putting Billy through this.

"I won't touch him," I chant under my breath several times, afraid to accidentally activate the safety before I've set Billy free.

I don't slow down once I get to the door. I kick it in and before the Commander and Mindbender can react, throw my three knifes at the hand restraints and the steel cable connecting the chair to the wall. Billy's screams subside into whimpers and he opens his eyes just in time to see me throw a knife handle first at the Commander's hand, knocking the device he just pulled out of his pocket out of his hand without harming him in the slightest.

"BILLY, GO! LEAVE ME!" I scream.

At the same time, I throw a shuriken at the Commander's device and my two remaining knives at the restraints around Billy's feet.

I don't see them reach their goal. Mindbender activates his own device and the pain drowns everything out.

"You owe your life to Snake Eyes, ninja," the Commander hisses. "I wouldn't need you if not for HIM."

He's so mad his eyes are actually dancing.

"Billy escaped, then, did he?" I ask, making my tone as casual as I can.

"I'll have him back," he growls. "You think this was a step forward for you, don't you? You think he'll tell Snake Eyes that you broke through the conditioning, and that your sword brother will rescue you?"

I don't answer. I hadn't really thought of that, but now that he mentions it, it IS a nice bonus that Billy should have been able to let my brother know I can still be brought back.

"He won't," the Commander hisses. "He's going to tell Snake Eyes what I told HIM: you will never be free. Even if you somehow end up coming back to your senses while we're too far to bring you under control, you will not enjoy freedom for very long: the chip is programmed to automatically activate the safety measure one hour after sending the alarm that the conditioning is completely off unless we stop it, and to keep it going. Mindbender figures you'd be dead within minutes. If you're ever free again, it will only be for about an hour."

Having said that, he turns on his heels and starts to leave, his fists still clenched and his heart rate still up from sheer rage.

It's funny in a way… he thinks he's just delivered my hopes a crushing blow, but in fact, he's just informed me Snake Eyes is now aware of what he'll have to do to set me free. Hopefully, my brother does a better job of going through with it than I did when I thought he was the one who needed to be put out of his misery.

"Q-tips," I announce before the Commander closes the door. He stops for a moment, curious as to what I mean, before he thinks better of it. "This is the fifty-third time," I explain. "Toothpicks would be too quick, I think, even if use the blunt end."

He snickers. "Dream on, Mr. Ninja. You're mine, and you will remain mine until I decide I don't need you anymore and kill you."

I snicker too, deliberately imitating him, right before the machine kicks in and makes me forget there are other things in the Universe than the pain I'm feeling.

Sixty-seven.

I try to focus my thoughts on trying to come up with a way to free myself, but lately, it has become harder and harder. It's like my brains are just tired of always thinking about the same unsolvable problems whenever they're actually in any condition to think.

It doesn't help that I keep coming back to the fact Snake Eyes could free me if he'd only get around to it. We've fought twelve times since Billy escaped - most of them in Springfield, finally - and he hasn't even TRIED to kill me. He really needs to stop procrastinating, too; the Commander has already started the preparations to abandon Springfield and move on to his next fortress. Pretty soon, Snake Eyes will no longer know where to even find me.

I do my best to try and think of an alternative solution to my brother doing his job - with the same lack of result as usual - right until Mindbender starts his machine and shuts down my capacity to think again.

I sit down with my lunch at the first empty table I see, only for another man to sit down right in front of me. I look at him curiously; nobody usually sits with me. He looks familiar, so I'm pretty sure he's one of the higher ups.

"Thank goodness I found you," he whispers softly.

I raise an eyebrow at him; I can't imagine why he'd be looking for me.

"The Commander is in grave danger," he announces, still in a low whisper.

I stop eating, my eyes wide. "How?" I ask urgently, getting up to look around. "Where is he now?"

"Shh! Sit down! He's not in danger RIGHT now."

I sit on the edge of my seat and fix my eyes on his. The dark makeup he wears makes them look unnatural, which only serves to irritate me more.

"Why is he in danger? How do I protect him?"

"Will you quiet down? If anybody finds out you've been warned… it'll be all over. He'll die."

My eyes widen again and my heart starts hammering. "Talk!" I breathe. "What's going on?"

"It's a very elaborate plot by GI Joe. I've discovered it, but I can't stop it. They have something planned against anything we may do to defend the Commander. I don't know what to do."

I gulp. GI Joe, setting out to kill my master, and we can't stop them? This can't be happening… I have to stop them, I can't fail him this time; I can't!

"I have to go to him," I say, getting up again. "I can stop whoever they send. I…"

"It won't help," he interrupts me, gesturing me to sit back down. "They're going to use some kind of weapon that you can't block, and they don't need to be close to him to use it."

I clench my fists and it's all I can do not to start screaming in frustration and despair. "Tell me what I need to do!" I mean it to sound like a demand, but it comes out sounding more like a plea.

"I figure we only have one chance. There is one person who is key to their whole plan; as long as she's around, there's nothing we can do to stop them, there's nothing we can do to save the Commander."

"And if she dies…?"

"If she dies before tomorrow, they will have to abandon the plan. The Commander will be safe."

"I can kill her. Just tell me where she is."

He sighs in relief and passes me a picture of a woman with flaming red hair gathered in a ponytail. She looks vaguely familiar. "She's a Joe," he says. "Her name is Scarlett, and she'll be there when we attack GI Joe later today."

"Scarlett," I repeat, staring at the picture, trying to steady my hands so it'll stop shaking. "We're attacking GI Joe?"

He nods. "You will remember, right? Scarlett must die, today, or the Commander will be dead by tomorrow night. Nothing we can do will save him if you don't kill her today, when we attack GI Joe."

I shudder violently at the thought. "I'll remember. And she will die."

"Good. Thank you. I knew I could count on you."

He smiles, gets up and leaves, leaving the picture with me. I glance at it one more time before tucking it in one of my pockets.

I can't stop shaking and after attempting a few bites, I give up on my lunch to go get ready for the upcoming battle. I can't fail this time, I just… I can't. I can't let my master be killed. Another violent shiver runs through me and my heart starts hammering a bit faster. I can't fail. I have to save my master.

I start looking for the red head as soon as we engage GI Joe, deliberately avoiding Snake Eyes. Each second that passes makes me more terrified that she's not there: she must die for the Commander to live. I don't remember the actual explanation, but I do remember that I MUST kill her, or my master will die.

My heart skips a bit and I grin in relief when I finally spot her. I rush her and much to my surprise, she manages to evade my first strike. I adjust and strike again, and this time, a blade held by a third person blocks mine. I recognize my opponent by sound; he's all too familiar.

I curse under my breath. Snake Eyes. Again and always, Snake Eyes!

"Oh no, you don't," I growl at him. "Not this time!"

He ignores me and places himself between the red head and me, his heart pounding just as hard as mine, and my eyes widen in sudden realization: I'm afraid because my master is in danger, and he's just as afraid as me because SHE is.

I'm no good at figuring things out, but this, I can understand; I AM feeling the exact same thing, after all. She's precious to him, just like my master is to me. This is how I can hurt him… I can't even imagine the misery I'd be in if my Master died, and I can inflict it on HIM. All I have to do is kill her, take her away from him. It's killing two birds with one stone: I can save the Commander and hurt Snake Eyes - make him cry like a baby, make him pay for every time he's made me fail the Commander.

I snarl at him and launch myself towards him, veering at the last moment to bypass him and strike at Scarlett. He blocks me, missing my blade but hitting my arm, deflecting it enough for my sword to only catch the girl's shoulder. She winces and tries to strike back, but all she accomplishes is to open her defences wider – I move to strike again, but suddenly hear Snake Eyes' blade moving through the air behind me.

I throw myself on the side, or rather, I try. In reality, I only manage to move by a few inches before the impossibly fast blade pushes its way through my back, coming out through my chest, its gleam hitting my eyes. The pain spreads out from the point it entered and blood fills my throat, drowning me. I try coughing it out, but more just keeps flooding my breathing passages. I collapse to my knees, the realization sinking in; I'm dying.

Images and sounds flood through my head, of another time. Snake Eyes, trying to kill me… I'm not hit, yet I'm in even more pain than now and for some reason, I can't believe he'd do that.

"Why… why did you?" I hiccup. I'm not sure who I'm talking to, it feels like I'm living two different moments, one of which is not actually happening to me and yet is taking over. The one where any hate I have towards Snake Eyes is gone, replaced by pain. I don't understand, why am I in so much pain if he hasn't hit me yet?

Even though it suddenly dawns on me that the pain I'm feeling is not physical but emotional, I've never felt so confused. Even though I can barely get the words out, I can't help but beg for things to make sense, I don't want to die without even understanding what I'm feeling. At the end like this, I'm terrified that if I don't even know my own mind, I'll be doomed to try and make sense of myself forever.

"Why… betrayed? Hurt…?"

Scarlett has no answer for me and as usual, Snake Eyes is silent. Yet I can't stop talking, or rather, I can't stop trying to talk - I can barely even breathe. I don't know why it matters, but I can't help myself: I need to know. I need to understand why it hurt so much. I need the closure, I need to clear this last bit of confusion.

Snake Eyes' heart is erratic. I feel worry grip me for a fraction of second before I remember he's fine, and I finally understand why it hurt so much when he tried to kill me before.

"I… care? For YOU? But you're… you just… you're always…"

And then, it feels like floodgates open. The memories wash over me, drowning me just like my own blood. I remember everything, from my earliest memories as a baby to Zartan, talking me into attacking Scarlett in the hopes I'll get myself killed.

I suddenly feel the ground against my upper body and the side of my face and although it predictably hurts, I chuckle: I'm free. He did it, he saved me. I almost feel like telling him off for taking so long, but he'd probably take me seriously if I did and feel bad about it.

"Brother… th… thank you," I manage to mumble before the silence claims me.