The end of the duel in chapter 24. Alister has summoned the Iron Giant—as in, humongous, lots of guns, red eyes, etc. It has 5,500 Attack Points and then got doubled to 11,000 and Mokuba has no cards to stop the attack. Alister is pretty much about to destroy the kid, and Mokuba gives us his speech as to why it wouldn't work. It implements the quote "You are who you choose to be", and adds that Alister didn't have to be such a monster who used machines to carry out his vengeance, but that he could also go in it in a peaceful manner. Unfortunately, it doesn't work and with three words, Mokuba is hit with missiles, lasers and guns (which is never seen but implied with a giant geyser of light show in the sky.
It got worse; before the attack, May—having been in pain chapters beforehand—begs Mokuba not to go with the sacrifice. Mokuba states that he has to do it, but thanks her and Max for being good friends and family. Then he goes to his brother, saying to take care of them while Alister unleashes the attack. The last thing that's said before his name is screamed? "Hit me with your best shot."
Then we find him in his soul room and meets up with his ancestor, who explains that even though it takes time, Peace would eventually radiate and take away the violence. Mokuba then returns, having been saved by a Trap Card that negated all battle damage and summons his Ancestor onto the field...to give Alister a hug. When Mokuba realizes what he's done, he says he forgives Alister, putting an end to one of the most powerful chapters in the story.