Thanks to everyone for contributing! :) Here's one split into three acts:
The Dragon Trinity:
Act 1: The Rifts
Rifts begin to open up all over the region after the Elite 4 are beaten. They cannot be interacted with and if you walk into one the screen will blur slightly. Once you see your first rift, professor <tree> will show up and worriedly inform you that such rifts have never before been sighted, and they are potentially dangerous. He upgrades your Pokedex so it can scan the rifts and asks you to scan 5 of them across the region before returning to meet him in his lab.
Every time you scan a rift, you will be attacked by a random level 70-75 pokemon from that area but fully evolved. For example, if there was one in the first route of Sinnoh you could be attacked by a level 75 Luxray. Afterwards, a passerby will inform you that the Pokemon you saw was far more experienced than any others in the area, and that the passerby thought he had seen that Pokemon step into the rift and come out much more powerful.
Upon returning to the lab, professor <tree> will scan your Pokedex and tell you that the portals are the results of space-time distortion. He guesses that the legendary dragons Palkia and Dialga must be involved, but he doesn't know how. He thanks you for your help and rewards you with the Adamant/Lustrous Orbs, telling you that these rare orbs may be able to call to their masters.
Act 2 will probably come tomorrow, if anyone's interested.
Jirachi: In your hometown, you are able to go into one of your neighbor's houses. In the house is a typical family, an older male NPC and an older female NPC and a young child NPC. The parents will talk about how imaginative, hopeful and full of life the child is. The child will say nonsensical, unbelievable things about different Pokemon and people. Post elite 4, at night time, you can speak to the child again, and he will talk about how he saw Jirachi on the TV, and how he would like to meet the legendary Pokemon, so he wrote his wish down on a piece of paper, and he asks you to read the wish. When you take the key item, the camera pans to the window, the sky flashes and a shooting star rockets across the sky. This will open up access to a part of an important tower or mountain in the region that was previously inaccessible. In this new hidden area, there is an abundance of steel and psychic types. When you get to the very end, you step outside into a new area, a small snowy square with a temple detached from the previous area. Enter into the temple, and you can encounter Jirachi. Engage it, and it will ask you to attach the child's note to its head. Upon doing so, Jirachi will awake and you can battle it? --- Formerly DoctorTitor None of us on this board are garbage! We are a GAMEFAQS, and we're darn proud of it! - MMX377