Every superhero has an origin story, a source from which his powers came. The world of City of Heroes is like a cornucopia of superhero origins; nearly anything is possible.
Ladies and gentlemen, the truth is that mutants are very real, and that they are among us. We must know who they are, and above all, what they can do!
--Senator Kelly, X-Men
Superpowered mutants are a fact of life; while not always trusted, the average person has become used to the fact that these people exist. Mutant powers arise from a freak of genetics, and can be inherited through family lines or affected by outside sources. Crey Corporation is known to have an extensive mutant research program devoted to cracking the 'X-Genes', as they're known, and developing mutant powers on demand. Mutants powers are inborn, and generally manifest around puberty; this doesn't always mean that mutants have an easy time controlling their abilities! In poorer areas, mutants may be persecuted or discriminated against; in Paragon City has produced the Outcasts, a criminal gang devoted to mutant supremacy.
Mutant powers have the 'Mutant, -10%' source limitation. Mutant powers are detectable to standard medical scanning in most first-world hospitals, and there are both antipowers and technological countermeasures available that suppress or remove them. Mutant intolerance is not common enough (or backed by enough legal power) to enforce a Social Stigma on mutants, however Intolerance (Mutants) is about as common in the US as Intolerance (Muslims), and with about the same geographical distribution.
Pepper Potts: I thought you said you were done making weapons?
Tony Stark: It isn't. This is a flight stabilizer. It's completely harmless.
Inventors since WWII have made numerous technological breakthroughs in robotics, computers, weapons technology, medicine, and nearly every other area of scientific research. Cold fusion is a reality (and Paragon City is powered by the prototype Terra Volta reactor); medical science exists that can cure most diseases, restore grievous injuries, or replace missing limbs, and they say that even human cloning has become a reality. A number of groups make use of advanced technology to varying degrees, from the Sky Raiders and their signature jetpacks to the Freakshow's deliberately crude cybernetics to the advanced battlesuits used by Crey's security forces.
Technological powers have the Technological power source (-10%). This includes Requires Maintenance (one person, weekly). Technological abilities are usually detectable by x-rays and medical scans, and will frequently trigger metal detectors, smell of oil or exhaust fumes, or get warm enough to show up on infrared. Technological abilities will frequently have one or more of Gadget (varies), Electrical (-20%), or greater maintenance requirements (varies).
Driver: Watch out for the weirdos, girls.
Nancy: We are the weirdos, mister.
Magic is very real, and various secret societies have been keeping it more or less under wraps for centuries. Hitler's obsession with the occult, however, unearthed all sorts of things that these groups would have preferred remain hidden. The Banished Pantheon in Dark Astoria work rituals to dark forces to try and bring ruin to the world; the Circle of Thorns seek to grab power in society by subverting the elite. The Carnival of Shadows claim to use magic only to entertain, but many feel they have more sinister motives, and the Minions of Igneous are clearly not simple natural manifestations.
Magical powers have the 'Magical' power source (-10%); anti-magic countermeasures exist, and while most areas of the world are 'normal' mana, the level will vary in some places while others may have 'tainted' mana. Characters gaining their powers from magical artifacts may add various Gadget limitations (varies); other magical abilities might have Environmental (varies), or Costs FP (varies). 'Requires Incantations' and 'Requires Gestures' are worth -5% each if you must just speak softly, or wave your hands about, or -10% each if you have to speak loudly and clearly, or perform more or less full-body gestures.
A variant on magic is Chi (-10%). Chi abilities are not affected by mana levels, but people with Chi abilities must maintain a fairly strict diet and exercise regimen; they have approximately 20 fewer hours per week due to time spent in meditation or exercising, and increase their cost of living by 10% to reflect the need for exotic foods, incense, oils, etc. This is effectively a Pact limitation to maintain 'Disciplines of Faith (Chi Rituals)'.
Let me get this straight: You think that your client, one of the wealthiest, most powerful men in the world, is secretly a vigilante who spends his nights beating criminals to a pulp with his bare hands. And your plan is to blackmail this person? Good luck.
--Lucius Fox, The Dark Knight
Some people simply train very hard to achieve the pinnacle in a given field, or are good enough with mundane technology to manage amazing feats. Others are truly aliens, members of a race with powers that seem fantastic to humans. Whatever the case, your abilities have become as natural to you as breathing. The Warriors are a gang who pride themselves on being 'pure humans' who can hold their own against groups like the Freakshow and the Tsoo; the mysterious Nictus claim to be otherdimensional aliens, and have energy control powers.
Natural abilities may not have a power source. It's frequently impossible to tell a master of the martial arts from any other fit human being, and difficult to take his abilities away from him. True aliens are still unlikely to suffer from detection or countermeasures if they look human, but some earthly substances may act as Mundane Countermeasures to their abilities for a -10% power modifier.