At the end of the Sky Fortress Boss, Eggman and Metal Sonic escape the collapsing armada to return to the Death Egg. Sonic and Tails look around frantically and find a single pod, prompting them to squeeze into it. Not only that, but the craft itself flies into space in a shoddy manner and you can feel how uncomfortable the duo is inside. When they leave, they take the existing pod, as well as what is presumably Eggman's pod, and their return journey is a lot smoother as a result.
Metal Sonic's speed and power may be unmatched, but throughout Episode 2, he displays bouts of incompetence that, while rare, manage to be hilarious. For example, If you don't beat him in the first act of Sky Fortress, he somehow manages to ram into a fuel tank of Eggman's flying fortress.
Eggman's display of trolling in Sylvania Castle's boss, where he reveals the twin arrow-shooting totems. However, instead of this being a boss fight rehash from Episode I, he summons the TRUE boss, which promptly smashes the totems.