Okay, so maybe this is a crackpot theory, but it's really making some sense, considering the links between HGSS and DPPt (especially Pt).
We all know Charon befriended Rotom when he was younger. The Secret Key lets us access the Rotom room in Pt, where Rotom's alternate forms can be found. Now, of course, it's in one of Galactic's buildings, so it's imaginable that a guy who works for them would have an office/development room for himself there.
Cyrus, of course, has a Master Ball, the most powerful Poké Ball. Now of course, there have been some theories on how he came to own one, considering its nearly-exclusive nature, but this isn't related to luck. In fact, the centerpoint to this is Charon.
In HGSS, if you have a Rotom first in your party (and not fainted, so it walks with you), walking into Silph Co. in Saffron will greet you with an empty lobby. But the elevator can be entered! Rotom takes you downstairs... and to a room that is exactly the same in almost every way (aside from entrance location) as Rotom's room in Sinnoh. The journals even mention that they were written by "the greatest genius in the world, Char..." This makes it obvious that Charon previously worked for Silph.
Three years before DPPt/HGSS, of course, was RSE/FRLG... and of course, the central conflict with Team Rocket is in Saffron, when they try to take over Silph for the Master Ball. Red breaks them up and stops their plot, and then is given a Master Ball by the President. Of course, it's a prototype, but that doesn't mean there's only one (and in fact, the lotto things in Johto, Hoenn, and Sinnoh prove that they are mass-produced, just much less than the others).
Here's my theory. Charon, tired of his Silph Co. work, and inspired by Team Rocket, stole a Master Ball and attempted to sell it. Now, go ahead and try this in any game. Gen I/II, you can do it, and get nothing for it. Gen III and IV, though, the Poké Marts won't buy it. Of course, with Team Galactic in Sinnoh, Charon sees his perfect opportunity, and joins it, giving the Master Ball to Cyrus so he can use it to capture Arceus.
Now another fun thing comes up. Porygon2 was implied to have been developed as an enhancement of Porygon, for space travel. Could Charon have been related to that project before he left? Possibly. In Platinum, the only Dubious Disc in the game is found in Team Galactic's HQ in Veilstone. Now, the Dubious Disc itself is at the very least implied to have been an unauthorized enhancement to Porygon2, but Porygon-Z's Pokédex entries imply much more:
DP: "Additional software was installed to make it a better Pokémon. It began acting oddly, however."
Pt: "Its programming was modified to enable work in alien dimensions. It did not work as planned."
HGSS: "Its programming was modified to enable it to move freely between different dimensions but something seems to have gone wrong."
Alien dimensions. That's exactly what Team Galactic's aiming to access, to find Dialga and Palkia.
SO IN SHORT
Charon worked for Silph Co.
Charon got Cyrus the Master Ball.
Charon developed the Dubious Disc.
And now we gotta fit the plot of RSE in somewhere, considering RBY/FRLG is connected to GSC/HGSS and DPPt, while Hoenn might as well happen 50 years after the rest of them, considering Oak doesn't even appear in those three.
We all know Charon befriended Rotom when he was younger. The Secret Key lets us access the Rotom room in Pt, where Rotom's alternate forms can be found. Now, of course, it's in one of Galactic's buildings, so it's imaginable that a guy who works for them would have an office/development room for himself there.
Cyrus, of course, has a Master Ball, the most powerful Poké Ball. Now of course, there have been some theories on how he came to own one, considering its nearly-exclusive nature, but this isn't related to luck. In fact, the centerpoint to this is Charon.
In HGSS, if you have a Rotom first in your party (and not fainted, so it walks with you), walking into Silph Co. in Saffron will greet you with an empty lobby. But the elevator can be entered! Rotom takes you downstairs... and to a room that is exactly the same in almost every way (aside from entrance location) as Rotom's room in Sinnoh. The journals even mention that they were written by "the greatest genius in the world, Char..." This makes it obvious that Charon previously worked for Silph.
Three years before DPPt/HGSS, of course, was RSE/FRLG... and of course, the central conflict with Team Rocket is in Saffron, when they try to take over Silph for the Master Ball. Red breaks them up and stops their plot, and then is given a Master Ball by the President. Of course, it's a prototype, but that doesn't mean there's only one (and in fact, the lotto things in Johto, Hoenn, and Sinnoh prove that they are mass-produced, just much less than the others).
Here's my theory. Charon, tired of his Silph Co. work, and inspired by Team Rocket, stole a Master Ball and attempted to sell it. Now, go ahead and try this in any game. Gen I/II, you can do it, and get nothing for it. Gen III and IV, though, the Poké Marts won't buy it. Of course, with Team Galactic in Sinnoh, Charon sees his perfect opportunity, and joins it, giving the Master Ball to Cyrus so he can use it to capture Arceus.
Now another fun thing comes up. Porygon2 was implied to have been developed as an enhancement of Porygon, for space travel. Could Charon have been related to that project before he left? Possibly. In Platinum, the only Dubious Disc in the game is found in Team Galactic's HQ in Veilstone. Now, the Dubious Disc itself is at the very least implied to have been an unauthorized enhancement to Porygon2, but Porygon-Z's Pokédex entries imply much more:
DP: "Additional software was installed to make it a better Pokémon. It began acting oddly, however."
Pt: "Its programming was modified to enable work in alien dimensions. It did not work as planned."
HGSS: "Its programming was modified to enable it to move freely between different dimensions but something seems to have gone wrong."
Alien dimensions. That's exactly what Team Galactic's aiming to access, to find Dialga and Palkia.
SO IN SHORT
Charon worked for Silph Co.
Charon got Cyrus the Master Ball.
Charon developed the Dubious Disc.
And now we gotta fit the plot of RSE in somewhere, considering RBY/FRLG is connected to GSC/HGSS and DPPt, while Hoenn might as well happen 50 years after the rest of them, considering Oak doesn't even appear in those three.