The griffons needed territory. Equestria had plenty of it. In a plan to separate Canterlot from their main ally, The Crystal Empire, the griffons conquer Ponyville.
Twilight Sparkle managed to put herself into a magical sleep in the basement of Golden Oak Library to escape the attack while the battle raged around her.
She rested for one thousand years, missing everything happy or sad, from Tirek's return to Spike and Rarity's wedding.
She wakes up in the middle of the night, surrounded by fallen beams and cracked stone.

Spike managed to escape.
On the run for two years before joining the rebels, he finally helped overthrow the griffon empire's hold on Equestria. Over the thousand year sleep of his surrogate mother, he has grown up, married, and assisted Equestria countless times. On a midnight flight, he finds a smoke coming from the chimney of the ruins of Golden Oak Library.