The first interaction they have, she begs him to save Ymir. He tells her that Ymir chose to leave on her own. Later we see Historia adopt this and agree, losing all her regrets.
In the cabin together she opens up about her true personality, and states that she admires Eren for being so sure of himself all the time. Eren says that he likes her new personality better and reassures her. Just a few pages later we can see a panel of her glancing at Eren while he looks at his key.
In the cave, she legitimately believed that refusing to sacrifice Eren would doom humanity, and she chose it anyway, declaring herself an "enemy of humanity". Considering how Eren has stated his intention to kill all his enemies dozens of times, they make quite the couple. (Not to mention she looks almost just like his father's first wife)
After that, Eren says that he will not sacrifice Historia, and there are sparks when he kisses her hand.
(earlier jean teases him about holding Historia's hand to remember things)
Not to mention the fact that Eren fiercely rejects any proposal to turn Historia into a titan, even when she suggests it herself.
And then Historia becomes pregnant just about the time that Eren leaves overseas.