Practically the entire main character list worked together to create this particular crisis. Henry found the key, Emma used it, Rumple provided the pen, and Regina got the ink.
This Author plot has a lot of theories swirling -- how much did he affect, when, and what was the effect of the Apprentice's spell on Emma and Lily?
Character agency is the ability of a character to make decisions that affect the story. That may be as simple as the decision to follow up on a lead that gives them information, or as complicated as a decision that puts their life at risk. Not giving characters agency is a common mistake for novice writers; things just happen to their characters, in ways unrelated to the characters’ efforts.
This is a writing error because agency is one of the ways in which you the writer make the audience interested in your characters. The decisions they make and things they do are the main way in which you show the audience who your characters are, what makes them unique and interesting and worth paying attention to. How those interact with the decisions and actions of other character is where you get plot.
If your character is just along for the ride through a whirlwind of circumstances in which nothing that character chooses to do has any effect on the story? At best, the audience is left wondering why bother with the character at all. At worst, the character is treated as an object in ways that reflect harmful social stereotypes.
Can your character be replaced by a presenceless narrator describing events? If so, you have an agency problem.
One takeaway from this is to treat plot elements that affect agency with care. Characters acting on false information, under coercion, or under more exotic forms of control available in an SF/F setting -- these are all options in the toolbox, but use them carefully in order to avoid frustrating your audience. If a character never has the right information, never knows what's going on, never gets to make an effective decision, is constantly treated as a puppet rather than a person who can affect the plot, what is the payoff for the audience? What is their reward for emotionally investing in what happens to that character?
Could your character be replaced by literally any other character without changing the events of the story? If so, you have an agency problem.
Herein lies the problem with the "Emma is good because of the Apprentice's spell, which is because of the Author" idea: it destroys four years of authorial work establishing her as a character. It would turn out that none of her actions tell us anything about her, only about the Power of Goodness that has invested her. Instead of a complicated, evolving representation of a person, we would have spent our time watching a shadow go through motions that have no human significance.
We feel invested in a character when they struggle to make a decision that will affect their future and their world. We feel zilch when we watch a computer program labeled "Achieve Maximum Goodness" execute.
The entire plot of OaAT to date has been based around the characters taking actions that affect their future, that change the course of the story -- a story that starts with Emma's decision to protect Henry's welfare. I'm not going to say it's impossible that the writing team is going to nuke the past four years of their work, but I consider it pretty damn unlikely.
