The first is Scorpius, not Harvey, sitting behind John as they fly through the wormhole. We're very aware that this isn't Harvey because of the look of wonder on Scorpius' face. It's this moment that makes us realize that Scorpius is at his core a scientist just like John.
Which brings me to my other favorite, when the command carrier is exploding and there's a rift of fire separating the two men as they face one another, and John says "We were close." Not just the connection of science, but also in the power of their individual convictions. Who's cause is the more righteous. We also get to see Scorpius realize just how far John will go and that he should have since the lengths are not much different than his own.
After Scorpius says goodbye, we see that John isn't as far gone as we fear by calling out Scorpius' name. As if he wants to apologize or offer up a ride...It's the remains of his humanity. It's also probably what prompted Scorpius later to decide and join John under the guise of protection. Anyway, the entire scene is just fucking gorgeous.