Ben and Gwen getting back together in the final chapter, where Gwen learns that Ben doesn't fault her for not being able to help him defeat Vilgax. The two kiss and make up. Literally.
They carve their initials into a tree, right next to the one their grandparents' had left behind.
Arguably, a good percentage of the story can be fit here, but in addition to the above, other notable moments include:
When Gwen, as a birthday gift for him, has Ben enrolled in karate, they run into the Girl Posse led by Marci, who accuses Gwen of being a manipulative control freak that runs people's lives. Seeing that Ben was in karate because Gwen's influence, this struck really close to home for her, causing her to run out of the dojo in tears. When Ben pursues her, she tells him that he can quit if he wants. Despite having spent the entire time leading up to his first practice complaining about karate, he refuses to quit, telling Gwen that they were a team. When Gwen wonders if Ben and her would be friends without being family, Ben points out that he's not very close to his friends, and that none of them would stowaway on an alien spaceship to watch his back.
The entirety of Chapter 11. Despite having been at each others' throats prior to learning of Ken's death, Ben is the only one in the family (who, to be fair, are wrapped up in their own grief and comforting others) to comfort Gwen, telling her that she would have made a great sister. She explodes that a great sister would have saved him, but Ben assures her that there was nothing she could do. Gwen in turn, assures him that there was nothing he could do. Ben then takes a stuffed animal that was going to be for Ken and gives it to Gwen for her to remember her lost brother, and Gwen takes a stuffed animal to give to Ben. Exhausted by the day's event, they fall asleep and end up in each other's arms.
Breaking Point:
Gwen dancing with Ben to the music of Jurassic Park during the Halloween party, to make up for the dance that Lucy had with Ben in Big Fat Alien Wedding.
Ben, during Gwen's first period. He wants to take care of her and likens it to how Carl feels about Sandra.
Ben feels that, once he puts the Omnitrix back on, he'll forget what it's like to have anything else on his arm. Gwen decides to kiss him where he'll place the Omnitrix, daring him to forget it.
