Emrakul hasn't been seen in a very long time. Worries of a possible attack on another plane lead Gideon Jura to Equestria, where he must hunt down Emrakul before the history of Zendikar is repeated.
Spike has never been alone, and even in the moment he was born he had Twilight... but that will not last forever, dragons have an extremely large lifespan, while ponies don't.