The storyline takes place two years after the current series of Soul Eater. This would mean that Maka, Black Star, Soul, Tsubaki, and anyone else in the series are far past 13 now, being 15, 16, etc.
Currently, The witches have been trying to figure out ways to summon a shinigami that they believe in legend, is able to overpower Death himself. They are unsure whether this legend to be true, but they will do all that they can, in hope for the Shinigami really existing. The Oldest Witch, leader of them all has finally died of loss in power. Three of the strongest witches have stepped up to take places as the Three Witch Lords. Two have been revealed. Darkove and Ryuuza.
A rebellion, known as "The Resistance", including meisters/weapons, witches, kishin, and enchanters that are against both the Witches Mass and DWMA is growing far more and it is beginning to concern Death. They believe that both the Witches Mass and DWMA are fortresses of an evil plot against the world, and they wish to bring peace to their country with thier own justice. They believe all criminals are scum and meant to be killed, regardless of being kishin, witch, or a normal human soul. They believe anyone who is apart of DWMA or the Witches Mass should be killed immediately on the spot.
The Weapon/Meister Academy is reaching a shortage of weapons and are currently searching for their now "endangered" genetically capable humans that can transform into weapons. Hoping to find any and taking them in, they are growing more nervous about the rebellions.
The witches were able to infiltrait the academy and get the information they needed. Darkove, a supposed Grim Reaper was actually a witch, and betrayed Death. He not only was a witch, but a Witch Lord. He, Ryuuza, the other Witch Lord, and several other witches had attacked the Academy and kidnapped the daughter of Darkove, who was a two-star meister, Emira Lefay, who is currently kept hostage at the Witch Mass and is in need of rescue as Death demands.
The Witches are growing stronger with their power and soon enough, they will be able to summon the shinigami they mean so well on. If the young meisters and weapons of the academy do not act fast, train harder, and get stronger, this could mean Darkness will reign over the world.