Team Knox is frustrated with the losses coming from a little 12 year old boy, and decides to take action. They kidnap his mom and dad, and tell him, that he must give them 100000 PokéCurrency in order for them to return his parents.
Of course that's just the gist of it, and I can add the "new move event" to it, so cyndaquil can save Silver's Parents or something along the lines of that. May will be part of this event, and that's all the spoilers I can give for now. Thanks for the ideas!
@siper x, have you tried just giving the ips file and the rom the same name and putting them in the same folder? If that doesn't work, LIPS is good, like Sonic Boom said, and has worked for me. If that fails you, first check that you are patching the GBA file and not a sav, bak, or pal extension. Next, make sure the Rom is clean, with no prior patches. If all fails, redownload the patch and try again.
And if that fails, take this to a help thread, which is honestly where you should have posted it in the first place.