Shiny's and Thunder's brotherhood in general. Over the course of the series, they go from fighting each other upon first encounter, to constant bickering, to a decent amount of respect for each other, to genuinely caring for each other's well-being.
Shiny and Thunder's reactions to each other's faked deaths. While it was just a prank, it was genuinely heartwarming to see them show how much they really cared about each other.
A Blink and You'll Miss it: During episode 10 when Alex is about to blow up the ORT and must once more be separated from her parents, Creed puts his hand on her shoulder to console her.
Thunder cheering up Shiny after Alex berates him. Even though they've only known each other for a couple of weeks at most, and Thunder has on multiple occasions voiced his opinion on Shiny being a good-for-nothing clown, Thunder still goes out of his way to make Shiny feel better.
The end of the episode Whack-A-Bot. Because of Thunder's sensors and personality matrix being messed up by the chemicals in the Kaiju cave, Shiny and Thunder come to understand each other better. Because of Thunder's warped sense of reality and altered personality matrix making him act, to put it plainly, quite stupid, Shiny now has to look after Thunder, which shows him how Thunder feels looking after him and why he needs to be so uptight. Thunder, on the other hand, learns why Shiny is often made upset by his uptight behavior, and apologizes for it. If that isn't wholesome, I don't know what is.
During the episode Upgrades, Shiny tries to tell Thunder how grateful he is to have him, even though upgrade rage is controlling him.
