Mitakihara Town, Japan. A modern-day city where nothing interesting happens. That is, as far as anyone knows.
Witches, beings made solely of negative emotions, prey on humans, inflicting upon them suicidal depression or murderous desires, feeding and making familiars in this fashion. These witches, unable to be seen by humans, threaten humanity if left alone.
Kyubey, a small white creature, a "Messenger of Magic", roams about the city in search of girls worthy of being magical girls. To these girls he offers a single wish before granting them their Soul Gem, the object that will allow them to use magic, see witches, and hopefully, save lives. The Soul Gems however require constant fuel; if slain witches' Grief Seeds are not used to replenish the used magic, the magical girl the gem belongs to could very well die.
Madoka Kaname is one of these magical girls along with some of her friends. Together they hope to free the city from the witches' grasp and defeat Walpurgis Night, the most powerful witch of them all.
But Kyubey is not telling them everything…