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I was planning on shiny hunting the legendary beasts in Soul Silver then whichever one I don't get I would hunt for in Heart Gold, but I wanted to hunt both of them AFTER I beat the game. However, no matter what I do, I can't challenge Morty in my copy of Heart Gold. I beat the rocket grunt in the Dance Theater but I still can't get in.

I've looked online and some say yes and some say no. I need to know for sure so I can be more prepared.

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You can test this in your own game. Just don't save after releasing a legendary Pokemon and you should be fine.
I was thinking about that but what if the beast I happen to release to test it out was shiny and I never knew? I don't have a level 40 pokemon OR repels(I have no money in that game)
You can just reboot the game.

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You have to release the beasts to challenge Morty's gym. When you go down the ladder in the Burned Tower, the beasts run away, then Eusine tells you about his dream to catch/see Suicune, then both him and Morty leave the tower, enabling you to challenge the gym

Source: Experience

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Aw man. Well, thanks for confirming it.