For all those who possess what can broadly be called "super powers," their abilities began somewhere. When creating a powered character, it is important to establish how your character got their powers, this is where the "origin" comes in. In addition to providing background to who your character is, it can also provide guidance onto some of the ins-and-outs of how your ability works and help you create your specific power modifier.
Below are some examples of origins that you can use outright, or from which you can base your unique origin. Note that some origins include required advantages or disadvantages, these too are guidelines, accounting for some the of the specific mechanics underlying the origin and may, with permission, be changed or omitted.
The following example origins are based on those that already exist in the setting. If used "out of the box" your character will be a part of some degree of existing (though perhaps not campaign relevant) events and changes in the setting. (That is not to say other origins won't have similar changes over the course of the setting, but these are already planned.)
You came from another planet (or even dimension!) and your abilities are commonplace for others of your species/kind.
All Aliens (both extraterrestial and extradimensional) require Unusual Background (Alien) [10] and Secret (Alien; Imprisonment/Exile) [-20].
The unusual background acts as a catch-all for justifying the unique biology, technology level, etc. that comes with your background (allowing you to have basically free range in deciding the specifics of your character).
The secret represents that within the current context, aliens are not publically known to exist and if you were to be discovered as one, would likely be imprisoned by government agents seeking information about your kind.
Your abilities arose as a result of a specific genetic mutation you were born with, making you a member of what some optimistic scientists believe is the next stage of human evolution, Homo superior. Other, more negative scientists (and quite a few members of the general public) might instead few you as a terrifying threat to the fabric of society. Who's to say.
All mutants require Social Stigma (Mutant) [-10] or Secret (Mutant; Rejection) [-10].
The current societal climate towards mutants is often negative, so being publicly known to be a mutant will expose you to bigotry, often from those you'd least expect it from. On the other hand, keeping it a secret may just be delaying the inevitable.
Your abilities
Below are some broader example origins. These examples lack the specific details and should be used as the foundation of a more specific origin for your characters' powers.
Your abilities come from an agreement made with a more powerful being. For some, this might be faith in a power-granting god. For others, an occult pact made with Something Man Should Not Know.
You should decide the "Who" of your pact and the specific relationship between yourself and the being who grants you your powers.
Example Power Modifiers:
Your abilities come from specific training to develop them. You can be anything from the member of some ancient monastic order to a trainee of a dark sorcerous cult to a student of an experimental organization.
Regardless of the specifics, you should determine who (or what) taught/trained you, what the discipline of your training is, and where you stand in relationship to your teacher(s).
Many origins of this nature should require Trained By A Master [30] or a similar trait to represent your training.
You abilities arose from a fantastical discovery (or invention!) you made. This covers both . Perhaps you discovered a superscience energy source to provide energy for power armor or discovered a powerful amulet to an ancient deity or so on.
You should determine what it is that you discovered or invented, what the greater context of that discovery is, and how you go about using that for your abilities.
You gained your abilities through exposure to some substance or energy. Perhaps a bite from a radiated creature gave you bizarre abilities, or you fell into a vat of experimental chemicals.
You should determine what the substance/energy/etc. was that gave you your powers.