I have a few ideas in my mind:
For the first episode, Twilight could be in the crystal empire and bumps into flash sentry again. Then twilight blushes and out of now where, a storm appers and this child falls from the sky and lands on Twilight and she sees that this colt looks like both of them. (Which is unknown to them is that he is their son from the future who has come to protect them from the evil in his time.) This is similar to sailor moon where Rinni appears and they don't know who she is until later.