Perhaps he is like a hedgehog or porcupine and the spines lie flat until he is agitated and they then pop up. That could be very embarrassing if they tend to extend with emotional states or triggers. 
Well, there's two ways this could go with the current spines model (if we ever get different animations, other explanations may arise):
1. The person rearranges their bone structure into spines that pop out. Only problem with this is that they'd have to, say, debone one arm cause they're whacking people with their humerus.
2. The person can generate excess bone matter, and that's the spines.
Either way, there also needs to be some explanation for why they don't bleed like mad with bone popping out of their skin.
Ok I'm going to take a poke at this (pun not intended) but I must say my mind works quite oddly some times so this may be a bit far reaching. That said, in a explination for powers sometimes the fantastic can be melded into compleate beliveability if it just sounds remotely plausable. My two theories are:
1) The mutants dermal make-up is different then that of a "normal" human, although outwardly he/she looks the same. Instead of an outer epidural layer, perhaps theirs is composed of a cartilaginous substance that can rapidly produce/reabsorb the spines. Also this could account for the power that alows them to "shoot" the spines outwardly. Could even say new spines could not be formed until such a thing happens. Not saything that this can't be a painful ordeal, but at least it's not a bloody one...
2) The mutation could be akin to cancer in nature. The skin again here being the entire cancerous growth. The spines are rapidly produced growths from the mass. The retraction of the spines is a reassimilation of the abnormal cells back into the mass. This would cause the projection of the spines to be violent rejections of being reassimilated. Much like a body might reject a transplanted organ. Of course this would be a controlled cancerous mass, that may or may not be harmful to the mutant, depending on where you want to go with the story.
None of that explains, however, how the spines somehow seem to not effect the heroes cothing...um...with rips and holes and such...hehe...logic? whats that? 
Great ideas! Thank you for the replies.
I have scribbled down your comments and will think about them some more.
As far as the X-Men like retraction from the skeletal system, I am completely shying away from that now. I watched her 'puff up' a few times in game and realized that the amount of spines is not explainable by being attached to her skeletal system and retracting. Just looking at the two huge scimitar-like projections (with several jutting branches) from her arms kills that concept.
It is almost like a transformation of sorts and less like extending these structures from their skeleton. But I cannot quite put my finger out in. Words like summoning and polymorphing do not quite work.
I can think of lots (and lots) of possible explanations for the spines. Whether they are plausible or not I'll leave to your own judgement of what is and is not reasonable. What you're really asking about are two things...
1) How do large spines like that come from inside you and through your skin without agonizing and/or grievously wounding you?
2) How do large spines like that come from inside you in the first place?
Here a few ideas just for starters (I'll start with the easy one, the skin...):
- The spines do not really go >through< your skin, you have subtle sphincter/pores that can open to allow their passage. Your clothes have well-designed slits, too.
- The spines are always outside your skin, they are just phase shifted/invisible and >seem< to shoot out.
- Yes they go through your skin, but not much of it, really. The damage is minor at best. Because you extend them so frequently, surrounding tissue is accustomed to stretching a bit out of the way. You tear up some of your clothes, but it's not too hard to stich the holes up when you're offline.
- It's a good thing you regenerate because otherwise you would probably be dead. You don't >seem< to take damage only because popping your spines also releases a boost of endorphins (like resist pain). That little boost of hormones keep you from passing out and gives you temporary hit points which are healed covertly during the course of a typical combat. You're clothing budget is through the roof.
Of course you can easily mix and match the clothing damage/personal damage options (I don't know why a scrapper >wouldn't< get special clothes unless they just didn't care - my spines scrapper just wears a skimpy outfit).
As for the spines themselves, let's look at why they seem ridiculous - they seem to be solid, branching shafts of bone longer than any other bone in the body. If they are extra bones, it boggles the mind how they could all fit in there. If not, it would seem like you wouldn't have much bone left.
So clearly the best way to make spines seem reasonable is to attack any of these assumptions about them. For example:
- The spines are not rigid, but flexible. Bendy tension-stuff holds them out like that. You really are whipping them at opponents or stabbing with them.
- What seems to be a solid shaft is actually two (or more) segmented ones. They move out at different rates, so joints that match up inside your body are braced on the outside. They also move away from each other at the ends, which is how huge branched appendages can go through a small hole in your skin.
- They are really your bones, but fortunately you no longer need your bones for support. You have a secondary skeleton/exoskeleton/cartilage/massive psychokinetic power that not only holds you up but gives you all those hit points compared to blasters and defenders.
- It has been demonstrated repeatedly that time is a relative thing. You grow your spines each time as a combined quirk of your regeneration and a form of self-affecting chrono-acceleration. Don't ask me exactly how you do it. (Though if you want to ask me, I can probably come up with something)
- The spines are produced through an unusual chemical secretion which hardens almost instantly on contact with air. This also explains why none of your wounds bleed... broken storage sacks instantly seal and brace any injuries.
- Your cells are not entirely differentiated. You are a sort of shapshifter... what seems to be spines is actually skin and other cells taking on a secondary, resilient function and being pushed into place by novel musculature. They do not break your skin because they >are< your skin.
- Your spines do not really physically exist. Their appearance is a byproduct of an ongoing energy generation/force field/mind control you manifest. Where does all that energy come from? The same place blasters (or controllers) get it! Yeah!
- It's not that your spines are strange, it's the rest of you. You simply do not have muscles and internal organs like everyone else, and so have plenty of space in there for spines, microwave ovens, extra sneakers, or whatever you may need at the time.
- Maybe it's not just your spines that don't really exist, but all of you. Your natural form is like a ghost or some other form of astral entity that can change at will but still interact with the real world. That's why bullets piffle right through you but a punch >really< hurts.
- As mentioned before, if your spines are out of phase/extradimensional/magically summoned or whatnot then none of this is really an issue anyway.
Well, you get the idea. Fun to think about (at least for me). Hope some of this is useful, or at least thought-provoking. Keep on arrestin'.
If I remeber correctly the offical explanation for Marrow (X-Men spines/bone weapons weilder) goes as followed.
Marrows power was to rapidly grow here bone structure, so although tey are her bones she is extending them beyond their normal limits and they peirce the skin as normal. The bone however could not be retracted and eiether had to be Cut off or extracted and another grown in its place. A sub-mutation was she was in capable of feeling pain due to a constant super high Endorphine level. Having said that she also had a healing factor.
The Cloths she wore were unstable molecules a marvel stable in which cloth is treated in such away it takes its dimensions and properties by being in contact with its wearers. They have long been a staple explanation in Marvel about how Shapeshifters cloths change with then, how the Torch didn't burn his cozzie off evertime and so on.
Hope this is some small assistence
If I recall correctly from my own Spines Scrapper, the spines do not retract, but instead disintegrate and crumble off.
It would then make sense that the spines are not piercing through the skin when they appear, but rather growing off of it. Of course, if it were merely a skin growth they would tear your own skin off long before causing damage to an opponent. So the growth must be on many layers from the surface down to the bone.
Wow! Some really creative comments, thank you 
To throw a total monkey wrench into the proceedings, she wants her Mutation Spines/Regen to be a Vampire 
At first, I was at a loss, but then I thought that it might work. After all, her secondary, regeneration could work with the vampire concept. And you all have helped me explain how the spines might work.
But could spines be a Vampire related power as well? Are there any vampire type myths/stories where the creature had powers such as these?
Thank you all again Fun posts.
Hmmm, spiny Vampire's.
Not if I recall but then again there are legends of a Vampire type creature that was a Head that flew around with its digestive system dangling down. Vampires can be almost anything.
Sticking a spike in someone and drawing blood through it makes sense, as does the fact that spines cause... is it slow effects? Obviously some poision secrected to keep the prey docile.
I don't remember any description of the Berbarang's(Bloodsucking creatures that attack people at cross roads) so yeah, I reckon you could go a distance with a Vampire. In Vampire The Masqurade the classic RPG of Gothic Moping there was a Branch of Vampires called the Tzimisce who did body shape shifty stuff like Bone blades.
Yeah if all else fails just claim it as a Brand of Vampire Unique to the CoH world.
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But could spines be a Vampire related power as well? Are there any vampire type myths/stories where the creature had powers such as these?
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When it comes to Vampires, about anything is possible, since they haven't actually been proven to exist. Somethings you could do:
-Vampires are known to be shapeshifters. They have been seen transforming into wolf, bat and even mist forms. It could be that this Vampire either has such control over her shifting abilities that she can form spines, or she just has some different form of shapeshifting ability.
- You could take a page from White Wolf's "Vampire: the Masquerade." He abilities could be like the flesh crafting abilities of the Tzimetzi (probably spelled that wrong) or the spines are just a really vivid dilusion of her's that she can project in to the minds of others, like a Malkavian. Also could be done via "blood magic" similar to the Tremer.
Indeed, the Tzimisce have an ability called 'Bone Crafting' that goes along with their other abilty, 'Flesh Crafting'. It's all part of a vampire Discipline (Power) called Vicissitude.
Flesh crafting allows the vampire to make flesh maleable like wax or clay. It's usually used for disguises, since you can craft yourself a new face.
Bone crafting allows you to fuse, pull, bend, re-form bones at will. I believe the higher level of the discipline is called Horrid Form - it allows the vampire to sprout huge spines all over their body. It also gives you enormous claws and strangely enough, seven fingers and black, oily skin.
Unfortunately, I'd go for Magic Scrapper rather than mutation scrapper - it's so much easier to explain.
Although, if you've watched Blade 2, you could explain it away as a mutation of the vampire disease.
That you three for the replies!
I do wish she had chosen Magic instead of Mutation. Is there any way to incorporate Mutation in being a vampire and still keep the mystery? I do not want to make it a 'scientific' alteration. That makes it so clinical and uninteresting
Well, she may have been a mutation scrapper to begin with, but after the Embrace (when a vampire drains out your blood and feeds you hers), she may have gained magical powers (the vampire stuff) since the power of the Blood is inherently magical - in most vampire settings anyway.
To back this up in gameplay, buy dual enhancements; Mutation/Magic.
It also makes for a rather intricate backstory.
I know you've got several replies for Spines, but try this one:
Think of it as cells stacking at an astounding rate from the skin, until they become the 'spines.' And yes, they seem to desintigrate, so maybe (for a origin concept) after a prolonged period the Spines become unstabled and the cells break down.
I do not have a background in comic books so bear with me please! I come to you all for help because you have such wonderful character concepts and stories.
Just for fun, I thought I would work on the background for my friends Mutation Spines Scrapper. But I first need to understand the archtype in a real world sense. Granted, you could easily just say it happens like magic! But I prefer to think it through a little as if this type of mutation existed (for the story).
What do you all think is happening when they suddenly puff up, bristling with boney spines? Do they have huge holes all over their body corresponding with the thickness of a fully retracted spine? They certainly do not appear to.
They are so enormous that it makes it difficult for me to conceptualize how they work. Especially the fact that the mutant looks normal and then suddenly she has fully extended spines that are completely out of proportion with her skeleton.
For example, I had to suffer through X-Men on a date once and the character with the retractable claws seemed fairly believable because it looked like it was possible for the blades to retract into the metallic sheath within his arms. This is not the case with Spines! They are immense and it is difficult to picture any sort of realistic biological skeletal system with instantly retractable spines much longer and larger than the bones in the leg (for example). One note, the Wolf guy in that silly movie had an innate regeneration and the claws actually pierced his skin when extending. This corresponds with my friends regeneration secondary so it is conceivable that his skin is being pierced each time: though the level of pain would be infinitely greater than the guy from the X-Men movie.
Can any of you come up with some fairly realistic ways of explaining the mechanics involved in a mutant with these prodigious spines?