The biggest question is where on Earth, or rather where on the Sun, does the energy that powers solar flares come from? This isn't an easy question to answer, but we're working on it.
Although we suspect that the Sun's magnetic field is a big part of the answer, there's a problem because we can't actually see the Sun's magnetic field directly. We have to rely on monitoring the way it controls the Sun's plasma. Images of the plasma show us that the magnetic field can be as messy as a bowl of spaghetti.