Have you ever wondered what Grisha was doing with Mikasa? Mikasa's father acts like Grisha comes over everyday, but why? I think that Grisha knew about the upcoming attacks on Wall Maria and tried to protect his son, the coordinate. The coordinate is humanity's only hope of surviving, and Grisha knows that. But the coordinate needs protection. What if he dies? That's what Grisha was doing. Turning Mikasa into a super strong soldier so that she can protect Eren, the coordinate. When he is done, he needs them to make a bond, so the super soldier has a reason to protect Eren. He takes his son with him to one of these visits, but finds out that Mikasa is gone and her parents have been murdered. Grisha tells Eren to wait for him at the base of the mountain while he 'activates' Mikasa's super strength. This happens just when Eren is in danger, and she kill the bandits. Grisha took this opportunity to adopt Mikasa, growing a bond between his son and her. Fast forward a year later, RBA attack, and shit hits the fan. Now Mikasa is protecting Eren until he saves humanity. And that's why Mikasa is so protective of Eren.

TL;DR: Grisha turned Mikasa into a super soldier so she can protect Eren until he saves the world.