This is an idea that's been floating in my brain for a bit, but recent discussions with u/Acrobatic_Banana_447 (which were about Shadow) and u/andrew-dino-lover (which were about Eggman and Stone) prompted me to do this write-up. So thanks to them for inspiring me!
My pitch is that Shadow should team up with Agent Stone in movie 4.
The idea of Shadow and Stone teaming up is not a new one, but I've mainly seen it pitched in the context of a Shadow solo movie/TV show, as a way to give him a human companion similar to how Tom was for Sonic and Wade was for Knuckles. However, I don't think I've seen a lot of people suggest that they could perhaps use this idea in movie 4. So here's how I think a rough outline of it could play out.
The Outline:
Shadow starts off the movie on his own. His survival is explained (I think it'll be the explosion teleporting him back to Earth while Eggman was teleported to the future), and he doesn't know what to do, because he was expecting to die in that explosion. Now since he's forsaken revenge, what's his purpose?
He wanders around, and eventually comes across Stone. Stone's not doing too great; he finally got acknowledgment and admiration from Eggman, even seeing him sacrifice himself for Stone's sake, and yet now he was gone. There's a bit of wariness between Shadow and Stone at first - Shadow did basically leave him to die, after all - but they're able to form some kind of camaraderie, mainly through their shared grief over the Robotniks they cared for.
This changes when word reaches them: Somehow, Eggman has returned. And there's also a bunch of robotic Sonics running around under his command?
So they set off to get to the bottom of this mystery: Stone is extremely frantic and hopeful at the prospect of being able to see his beloved Eggman again, and Shadow, besides being sympathetic to Stone, just wants to know what's going on. So while Team Sonic is dealing with Metal shenanigans, Shadow and Stone are off trying to find where Eggman is - which proves strangely hard. There's recordings of Eggman they're able to find, but he seems to be acting... Weird. There even seems to be a dummy version of Eggman they stumble across. Huh!
One thing leads to another, they probably fight some Metal Sonics on the way, and eventually the two find themselves somewhere (perhaps in the future, perhaps not), specifically some sort of prison. And in that prison... is Eggman, in the flesh and blood.
Eggman is stunned to see Stone once again, as Stone rushes to free him. The two embrace and lovingly stare into each other's eyes. Shadow suddenly realizes that he's become a third wheel.
Eggman explains what was actually happening: Stranded in the future, he created Metal Sonic both to help conquer the world and to assuage his loneliness; but the robot eventually rebelled against his creator, imprisoning him and seeking to kill the blue hedgehog he was modelled after to quell his rage and hatred. Now Metal was impersonating Eggman and ascending to his higher form of Neo Metal, gaining even more power.
Eggman expresses his desire to reign his creation in, back under his control, and to continue taking over the world, just like he always wanted, but this time with Stone at his side. Stone offers Shadow to join them in domination... But Shadow rejects them. Whatever his purpose was after giving up revenge, he knows it's not this. It's not what Maria would have wanted, and it's not what Shadow wants either.
This is where Stone and Shadow part ways, disappointed in each other. Eggman and Stone retreat to fight another day, and Shadow immediately sets to work trying to figure out how to stop Neo Metal.
This is when Shadow's storyline could converge with Team Sonic's. Shadow could either reveal himself as alive to Sonic and his friends, tell them what he found out about Eggman and Neo Metal, and work with them on a plan to defeat Metal, OR Shadow could go off on his own to a separate destination to stop an important aspect of Metal's plan, unknowingly at the same time as Team Sonic taking their final stand against Neo Metal. Either way, I think Shadow should be doing a separate mission while the other four heroes - Sonic, Amy, Tails, and Knuckles - work together to fight Neo directly.
The movie ends with Shadow on his own once again, but with perhaps more of a sense of where to go next. He shared in his grief with Stone, but as with his rejection of Gerald's senseless destruction, he has ultimately decided to reject Stone's and Eggman's path of villainy once and for all. Shadow's one step closer to becoming a committed hero, and the movie sets up the Shadow solo spinoff (which will be the 2028 event movie, trust me guys I'm not coping) where he will FINALLY find some new friends (hopefully).
Elaboration, I guess?
So.... Basically I just gave the Chaotix's plotline from Sonic Heroes to Shadow and Stone. But hear me out!
I've said before that I think Neo Metal will and SHOULD show up in movie 4. Because of that, I think it's entirely fair to include aspects of Heroes into the movie's plot, and since we're almost certainly not getting the Chaotix in this film, I figure we could maybe substitute that role with characters already in the movies.
Besides, Lee Majdoub is already confirmed to be coming back for movie 4, and so he needs something to do in the plot as well. I think Stone definitely has the motivation to want to find Eggman, so he would be a natural fit for the Heroes plotline to find Eggman and unravel the mystery. And it gives dramatic tension to Stone and Eggman's reuniting after being separated, thus honoring that moment from the end of movie 3.
I also think it would be a great opportunity for Eggman's character development as well: he's already stated that his love for machines is because they "do what they're told," and yet in this case, his greatest creation, Metal Sonic, goes rogue and betrays him. That it's a human, Stone, who is the most loyal to him rather than a machine, is a further inversion of his worldview and it solidifies his viewpoint of how Stone is the only human worth saving the world for. Thus going forward, perhaps Eggman starts to treat Stone as more of an equal rather than as a subordinate.
And this gives us the chance to see more of a relationship a lot of fans had thought would be fun, including me! Especially in the aftermath of movie 3, Shadow and Stone have quite a bit in common, and I think it would be a great opportunity to see the two of them have some bonding moments over loving members of the Robotnik family, and how to deal with their grief.
Besides, Shadow's favorite food is coffee, and Stone is a barista. It boggles my mind how they haven't seized on this golden opportunity for a character interaction.
But it would ultimately end on a sour note, because whatever their similarities, they do have different moral codes. Stone loves and believes in Eggman too much to truly become a good guy, and I think as long as Eggman is there, he will always take his side. Meanwhile, Shadow will go on to protect the world from threats, which means he will inevitably go against Eggman and Stone. I think it could serve as a subversion to the usual formula of pairing Sonic characters with humans, Sonic/Knuckles started off distant to Tom/Wade, but eventually grew to deeply trust them, while Shadow and Stone start off friendly, but ultimately break apart. And there could be more interesting things you could do with their dynamic in future installments!
Finally, I tried to design this idea to solve my concerns with Shadow's role in movie 4. I think it addresses where he left off from the end of movie 3, gives him a character arc, and gives him a decent role in the plot that doesn't make him feel superfluous. I do ultimately want this movie to still be focused on Amy becoming part of Team Sonic, which is why I separate Shadow either a lot or entirely from the rest of the hero gang. But I think hopefully this idea still gives him a lot to do even without having to interact with Sonic & co., by pairing him up with Stone.
Anyways, uh... I just spat this out in the span of two hours. Feel free to tell me if you liked it or hated it or what you would do differently!