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It's basically what Toby said Dan -

The Sonic X comic takes place in a nebulous period after the end of Season 2 (The Sonic Adventure 1, 2, and Battle arcs) and very beginning of Season 3 (The Space Saga) making it in continuity with the show more or less.

Because of this decision, Shadow was not around during this period due to his death in the SA2 arc as he did not come back until somewhere around the beginning of the Space Arc (his presence in the universe of the SX book would have been a major continuity error). The decision by Sega and Archie to have the SX comic take place in between those seasons was mostly due to necessity and tone. Sonic X in general was a light-hearted show at its onset and the comic reflected that albeit in goofier regards to some degree. But I think that the general consensus among those executing the book was that because of this, nobody wanted to deal with the Space Arc in the comic - not because it was bad at all mind you, but because Season 3 was pretty heavy and much darker in tone compared to the rest of the show. So the Sonic X comic in general went off a mix of the happy, goofy Sonic X/early Sonic comics approach and in doing so and staying true to the continuity, it meant Shadow stories in Sonic X were off limits A) because Shadow is always a pretty grimdark character anyway and B) he was already featured prominently in the main comic also.

Since te main comics had Shadow as thier exclusive, it's also why SX had Cream, Cheese, and Vanilla as thier exclusives. Since SX is dead now, that means Cream and co. can now be introduced in the main comic in the future, but don't expect that to happen anytime soon.

Anyways - I'm getting off topic. Since Sega and Archie decided to end SX to bring about Universe, it meant the final issue kind of got to throw the rules out the window and one of those was allowing the use of Shadow for one story. To maintain the continuity that "Shadow is dead during this time period" and not break what was established, Ian decided to use Shadow from the main universe. Since Main-Universe Metal Sonic was built with the ability to jump zones, they'd have Shadow and MS port in, say hi, and make it a cute fluff-piece-going-away-issue that fits into the tone of how the book itself was presented - lighthearted and cute. The key point being: You don't have to read SX40 at all to follow the plot going on in the main book. Think of Shadow's interlude as a tiny side story to the prime series, and nice way to say goodbye for the SX series by breaking its cardinal rule of "Shadow off limits cause of continuity". Heck - to make it even easier, if you never read it to begin with you'd think that SU #1 starts off immediately after the point of Hedgehog Havoc where he dissapeared none the wiser.This makes both parties happy.

AS FOR SHADOW'S DEATH:

The main complaint I always hear is the usual one with Sonic X: Chris Thorndyke's role in the show.

For the SA2 adaptation at least, Chris basically replaced the role that Amy had in the games. Amy wasn't playable in SA2, but she had one of the most important roles to the plot - talking face to face with Shadow, getting him to see that what he was doing was wrong and that the courses of action he was taking was not what the dead Maria Robotnik would have wanted at all. That scene, near the end of the game, was crucial character development for both "Revamped Amy" and Shadow at the time because it let us know there was a truly compassionate person behind her "giggly hyper-crush fangirl" persona (she took a risk approaching him one on one on Space Station Arc) and that Shadow's beginnings as a character boiled down to being more "misguided direction" than "flat out evil". The main complaint I'd always heardf for this is that by having Chris steal Amy's spotlight during that scene, it cheapened the role of Amy and the impact of what it meant for both characters.

It was played out exactly the same as in the game as it was on the show mind you - it's just Amy's shining moment was now Chris's shining moment for the sake of making people like him - and that soured quite a lot of people who really liked that Amy finally had that shining moment to make her a fuller character to begin with.

This course of action did allow one major direction that the games never dealt with, though. Whereas Shadow's death in the games eventually meant dealing with his convoluted reintroduction and origin, in Sonic X it meant that Chris - who was always presented as a sensitive, naive, quiet, and all around lonely kid anyway - took said death, and the loss of a potential friend incredibly hard. The more lighthearted and take-it-all-in-stride SX-Sonic knew just how much which is why he made the detour to show this "different Shadow" to Chris to begin with (largely because he knew seeinghim alive somewhere would cheer the kid up). It made the scene all the more funny and poignant when Chris sees Shadow and naively bursts into tears while Prime-Universe Shadow's reaction was the equivalent to "WTH?!?!"

When SX-Shadow was finally reintroduced during the space saga it was very much a big deal to Chris and all the other characters who'd figured thier Shadow had burnt up in Earth's outer orbit just as we had assumed once upon a time.

Anyways - the stasis chamber you see Eggman standing over (which holds the true SX-Shadow) is the same one you see him standing over at one point in the Space Saga during Season 3. Since the SX comic never referenced anything in Season 3 you can consider that scene another easter egg for the fans of the show who'd often asked was there anything that linked the book's nebulous point to the seasons it sits in-between. And I think that covers everything. Someone else can elaborate on anything I missed if they see fit.