I am very glad you asked this question, because there is an excellent answer for you. This exact scenario has been explored rather beautifully and in elaborate detail in the novel "Grail", an alternate to X3 written by an author with the pen-name of "minisoonoo". She too wondered what it would be like if Jean came back totally good, and she whipped up quite a masterpiece:
Should you wish to read it, you can find it here:
http://www.themedicinewheel.net/grail/grail.html
In this version, The Phoenix is Jean after having had her mutation reach completion. Interrupted by her traumatic experience with her best friend's death, Jean's mutation completed when Jean was exposed to Magneto's machine and was fully manifested at the moment of her death. Her comeback is drawn out and complicated than it the movie, and involves her first accidentally taking on a wrong identity (she literally didn't know who she was and no longer had a body, so she picked a wrong body), but eventually all that's sorted out and Jean is brought back home and given a tearful, heartfelt reunion by all her friends and family and students.
She's the good Jean, she's fully in control of herself, and she's back. Sounds like a boring story, huh? No conflict, eh? Oh you'd be surprised.
Jean's return causes at least 4 conflicts (at least 3 of them significant) to appear and each gets its own story arc:
1. Jean needs to come to grips with what happened to her and what she's become. She doesn't know what she is anymore. Warren points out to her that
the last person who came back from the dead was the son of God. So what does that make her? She talks to different people about it, and each gives a different answer (One good answer: You are Jean Grey). Being potentially immortal has its benefits, but it disturbs Jean knowing that she's going to outlive them all, including the love of her life, Scott. That she'll being drawn away from this world and to a place that no one else can follow.
2. The temptation to use her powers. Jean keeps discovering how powerful she really is, and with her knowledge of medicine is able to pull off some amazing things. She is tempted more and more to use her powers, it becomes rather convenient and addicting. BUT WHERE DO YOU DRAW THE LINE? When should you let matters run their course? Just because you have good intentions, does that mean you should go through with them? When should you interfere and when should you butt out? And at what point do you become so dependent on your powers and hate the limitations of being human that you essentially stop being human? If you have the powers of a goddess, should you act like a goddess? If you can solve all the world's problems, should you?
And there is the danger of her losing her temper. When she gets mad, her eyes glow, the flames appear, and stuff ends up being hurled and tossed around. At one point she nearly shook the whole school apart!
Fortunately, she has people like Professor X to guide her. She may be more powerful than him, but his wisdom and experience surpasses hers. And she still has Scott to lean on. As Scott points out to her: "I'm afraid of what you can do, but not afraid of you, because you're still Jean Grey". And what wisdom does Xavier give her? To be guided by her compassion and humility, her love of life and love for the people around her. That if she fears something and hesitates, that is a good sign. That the more she fears, the less HE will have to fear. She is a child that has outgrown him but he feels confident that he taught her well and she will cope. It's a learning process. Sometimes she succeeds, other times her good intentions end up blowing up in her face. But Jean learns.
When others express their concerns, Xavier describes Jean as follows:
"She may no longer be what you and I consider mortal, but she is still human".
3. Why did Jean get off the plane, and why did she allow herself to die? There are several reasons. Scott is convinced that she did it because she wanted to commit suicide and to get away from him. He's convinced she wanted to leave him and it causes him terrible pain and anguish. Jean herself doesn't remember why. Or does she? Did she truly forget? Or is she holding back somthing that she DOESN't want to remember? She comforts Scott by telling him that she CAME BACK BACK FOR HIM, because she loves him and missed him. It's comforting, but not enough. It's a major conflict that is explored throughout the book, and the true, ultimate answer is finally revealed towards the end, when Jean tries to run off again, having realized she's become too powerful to be allowed to live. And Logan exposes the truth to her: tells her WHY she did it at Alkali Lake, and why she's really doing it again. She realizes that Logan is right...
4. The simple fact that Jean was dead and is suddenly alive is a major complication. It's been 8 months. She had her memorial and grave, and the school moved on. They also went to alot of trouble to arrange for the authorities to acknowledge her death, so no one would get suspicious. Missing persons reports had to be filed, and a car had to be dumped into a river claiming she was the driver. Now she's back and all that has to be changed. And it's definitely not easy. And no you can't simply enter everyone's minds with Cerebro and change their thoughts around. Paperwork needs to be filed, evidence needs to be removed or replaced. It turns out to be a complicated process! Especially when Jean really needs to appear in public and they all know she can't be seen by the outside world until the mess is cleaned up.
As to what kind of threat they have to face? It is one that is subtle at first but eventually overwhelms both the X-Men and the Brotherhood and challenges all of Jean's abilities as a doctor and as the Phoenix. And you're probably wondering, if Jean is so well in control of herself, how could she possibly go dark? She does go dark, but not for any reason most people would ever think of. It's not due to mental manipulation, or built-up rages, or mental blocks.
She goes dark, becasue of her love for her friends and family, the kids at the school (her children). They're either dead or dying, there is nothing she can do to save them in time, and the bastards responsible for this are laughing maniacally in her face. Oh she goes dark. She completely loses control and gives in to her anger and helplessness, because she loves them and wants to save them. She takes on the villains in the story and it's a titanic, colossal show of course. Either they'll give her what she needs to save her children, or she'll destroy them all. And it's another one of life's lessons, as Jean learns that acting out of anger doesn't solve anything. She regrets what she does, and realizes that it accomplished nothing.
And while she does this, her teammates mount a mission of their own: one to save those who are dying, and the other to save Jean. They realize correctly that she's not a monster who needs to be destroyed, but a person who needs to be saved and brought back to her senses. They succeed at both, and Jean is able to redeem herself, using the full extent of her compassion and the Phoenix powers to save the day, but it costs her her life...
The Phoenix cannot ever die. She is always reborn. But she can choose to NOT come back. And now Jean realizes she has become much more powerful than any human should ever be allowed to be. She is dangerous to herself and to those around her. She could kill them all if she ever were to lose control again. So she has a difficult choice to ponder. Maybe it's time to let evolution runs its course, and take her to that next level of existence beyond the grasp of humanity... Except, there's one lingering thought left... she would miss someone... someone that she loves, someone that she made a promise to never leave...
What choice will she make?
I'll let you discover that on your own (unless you want me to spoil it for you), but I'll end this with my favorite quote from the book:
There is ever, only one phoenix.
Except when she refuses to rise.
The phoenix must live without mother or father,
without kith or kin, without mate. She is alone.
And that was beyond bearing.
In choosing mortality, she chose companionship, and love. And it's only love that can kill a phoenix.
In the acceptance of death, she found her true rebirth -- and her salvation.
In the acceptance of death, she found her own grail.
Her final fate is one that doesn't involve either death, or mental blocks, or the Cure, but something far more unexpected and... appropriate.
As an alternative to X3, I found Grail to be much more in-depth, intelligent and engaging, and the ending was very surprising but much more appropriate and fulfilling.
Also keep in mind that Jean may have the powers of a goddess, but she's not omnipotent. She doesn't know about everything at the same time. Mystique still manages to pull a few surprises on her. She can't predict the future. And Scott can still block her out of his mind if he chooses to. She still needs to sleep and eat, she still can get drunk, if you pinch or cut her she'll still bleed and it'll still hurt.
In fact, as the story unfolds, she realizes that she LOVES being human. Having super powers may have its perks, but she doesn't use them as a convenient way to fix everything (although she could). She can blow up entire city blocks, but can be very gentle and heal your wounds too.
But when you hurt her feelings, she cries. And when she's afraid or upset in danger, she still leans on Scott because she knows she'll always be safe in his arms.
And THAT is how you can do a Phoenix Story that involves Jean being good and in control and showing off her true strengths and compassion. This is how you can have her go dark and not be seen as a monster, and this is how you can end up with a story that's still suspenseful, full of action, and with an ending that you'll never see coming, but still appreciate.
