Any moment where Megatron is kind. The moment where he and Soundwave decide for Decepticons's creation and symbol is kind of cute.
The chapter 9 is full of this. At this point, Soundwave is just broken because Frenzy dies and Rumble is reformatted and would never be the same anymore.. Everyone is just damaged by what happened yet when Megatron looks like he is about to punish Soundwave for his mistake, his cassettes are all there and ready to defend him from Megatron. It just shows they aren't just like a family. They are a family.
Orion Pax's speech to Soundwave in this chapter. He just informs him how Megatron was worried for his safety.
The moment between Megatron and Soundwave...Just...heartbreaking.
"We've been friends for a long time Soundwave. I thought I understood you. You were a fierce warrior, with a strategist's mind, stoic and wise and powerful, but with a nurturing side as well. I admired you, Soundwave – more, I worshipped you. You told me once that mechs were superior to gods, but you were my god, Soundwave. You had all the answers, you were invincible, infallible, even when at your worst, it was on your own terms – no one could bring you down."
Chapter 13. Soundwave finally got his revenge on Ratbat as well as on the guard who killed Frenzy. In the ending, Megatron leaves the Tower while carrying Soundwave in his arms, bridal style.
Chapter 14. When Soundwave awakes, he is immediately welcomed by his Cassettes. Later, Megatron eventually visits him. Not only he scolds Shockwave for not informing him that Soundwave was up, but the two of them share a Held Gaze moment. It is ruined by Shockwave though.
In the same chapter, there is their sparring session which is full of companionship with a bit of flirting. When Soundwave points out Starscream's interest in Megatron, this latter asks him about his point of view. Looks like Soundwave's feelings aren't so one-sided.
