Is there a way to start the whole story thing over? I mean I made a bad choice and lost to some 5-star enemies. How can this be reversed?

losing a battle has no impact on anything. You can just. try again. You can't get permanently stuck in this plotline unless you just entirely give up instead of trying to figure out what went wrong.

If you lose a fight, you want to consider what happened- what about the battle wasn't working?, and consider your pets- number of party slots you have unlocked (2 in viridian meadows areas, 3 in umbra forest), pet elements, party order, proficiency points, and equipment.

Other players are often willing and able to help work these things out.
What pets are you using for the fight?