[4] From Sonic06 onwards, Shadow never re-learns the extent to which Rouge and Omega care for him and continues down a self destructive route of pushing everyone away. This timeline, the main canon timeline, is his bad ending.

[3] Shadow is only able to beat Mephiles through teamwork after realizing that Rouge and Omega not only care for him but would gladly die by his side. That's a great character arc for him... But that whole timeline got wiped from the canon.

[2] In Sonic06 we watch Shadow do his typical "I'm the coolest, I don't need friends" bit the whole game. However, through the events of his story he realizes that this whole time he's been friends with Rouge & Omega and didn't even know until the cards were down and they didn't fold on him.