1. There's the future Sonic going by an alias, scared and forced by circumstance to lie to the people close to him.

2. The way the other characters were affected by his absence.

3. The backstory with the gods and the quest to find them.

4. The time travel plot with Silver (wich includes some existential stuff about identity).

5. The history of the world, the war, and the internment of "conductors"