Now that Koutarou and company are back from their long journey to Forthorthe, everyone is hoping to settle back down into their normal, peaceful lives. Things are quickly thrown off course, however, when Theia, Ruth, and Clan show up with a little extra baggage and Koutarou suddenly finds himself in the midst of intergalactic negotiations. Has the real alien invasion just now begun? And what’s with the strange voice Sanae keeps hearing? Moreover, what’s got Clan so pensive?

With one of their own in trouble, Koutarou and the others are left reeling. Clan thinks she may have gotten to the bottom of things, but if what she says is true, the crisis they now face has been in the making for thousands of years. But the surprises are far from over there. A strange message for Koutarou could mean a tentative new alliance with a most unexpected partner. The offer comes at a time when they could desperately use the help, but what will the true cost be?

Just starting high school, Koutarou is moving out on his own to take some of the burden off of his widower father. Lucky for him, he's found a room at Corona House. It has a great landlord, it's not too far from school, and best of all, it's dirt cheap. It really is perfect... except for the strange girls that keep appearing to try and take it over! But even as room 106 turns into a battlefield, Koutarou isn't willing to give up his apartment without a good fight. The invasion begins!

Nana comes to Clan, Harumi, and Theia for maintenance, but it turns out each of the girls has something they want to improve on. After Alunaya sees a commercial involving hot spring eggs on TV, he wants to visit a hot spring to try some. He and Shizuka go together with Ruth and Kiriha on a weekend getaway. Sanae and Theia get competitive over a local eating contest, and if there’s food involved, Koutarou and Yurika are never far behind. And then Yurika has to study for an exam?!

Now that the invaders have come to an understanding of sorts, things are going smoother than ever in room 106. Spring is in the air--tulips, friendships, and potential romances are all about to burst into full bloom. Koutarou and the invading girls have never been happier together, but nothing lasts forever. Things turn dark quickly when they find out that they're going to have to say goodbye to one of their own... and soon. Without even any time to prepare, will the bonds they all share be enough to pull them through?

The evil magical girls are finally making their move to seize the mana pool in room 106, just like Yurika's been saying all along! Koutarou crosses paths with an old enemy, and Maki is forced to decide whether she follows her duty or her heart.

After Clan and Koutarou are caught in the premature explosion of the Super Space-time Repulsion shell, they're blown clear across the universe to a most unexpected destination. Will they be able to put their fight aside long enough to cooperate and figure out a way to get back home? Along the way, they'll meet some strangely familiar allies and witness the start of a legend firsthand--just not the way they ever expected it to happen.