Because Marvel Studios doesn't have the rights needed to call any of their characters "mutants" - as that power entirely belongs to 20th Century Fox - we have spent months and months wondering exactly how Aaron Taylor-Johnson's Quicksilver and Elizabeth Olsen's Scarlet Witch gained their powers in the Marvel Cinematic Universe. We expected that we would have to wait until the release of The Avengers: Age of Ultron to get the answers, but fortunately they have now arrived a bit early - in comic book form. It turns out that it all links back to Loki's scepter
Newsarama has the scoop on a new "One Shot" being published by Marvel Comics that will serve as a prequel to the Joss Whedon-directed Avengers 2 and explain exactly how Quicksilver and Scarlet Witch get their powers in the MCU. According to the story, everything really unfolds thanks to experiments being conducted by Wolfgang von Strucker (played by Thomas Kretschmann in the movies) - who we first saw in possession of Loki's aforementioned scepter during the post-credits sequence of Captain America: The Winter Soldier.
In the comic, Struker begins doing running tests on residents of a fictional European city called Sokovia, hoping to use the scepter to "unlock" any inherent powers that they may have. This is how he winds up meeting the twins Pietro and Wanda Maximoff, who wind up gaining super speed and reality manipulation abilities, respectively.
As Newsarama points out, the use of the term "unlocking" suggests that these powers were already inherent within both Quicksilver and Scarlet Witch prior to their medical experiment experience, but that of course begs the question of exactly what Loki's Scepter really is. Fans have been suggesting for months that they may just be Inhumans - which could suggest that the glowing blue rock in the God of Mischief's staff is some kind of Terragen Crystal - akin to what we've already seen on Agents of S.H.I.E.L.D. The problem with this theory is that Marvel Studios President Kevin Feige has already denied that Quicksilver and Scarlet Witch are Inhumans, and this idea also doesn't explain why Loki was able to use his staff to hypnotize Hawkeye (Jeremy Renner), Erik Selvig (Stellan Skarsgaard) and others in the first Avengers.
The other theory going around is connected to the concept of Infinity Stones - which we learned a lot more about this past summer in Guardians of the Galaxy. In Joss Whedon's The Avengers it's clearly stated that there is a connection between the Tesseract and Loki's scepter, and it's possible that the stone's natural abilities is what leads it to bringing out Scarlet Witch and Quicksilver's powers. Of course, exactly how this happens is still a mystery.
So now we obviously have the "how" when it comes to the question of Scarlet Witch and Quicksilver's powers, but we are still left a bit puzzled about the "why" angle on it. For that explanation, it seems that we will have to wait for The Avengers: Age of Ultron to hit theaters on May 1st.