Like in every other Pokemon game, D/P has some Legendary Pokemon in it. D/P has the most Legends in it's game (Not including Events). This guide is on how to get the Legendary Pokemon in-game not including the Event Pokemon.
These are the Pokemon that each game is based on. After you have done all the stuff in the Galactic HQ in Vielstone City, you now go the bottom entrance to Mt Conranet (The one that connects Hearthome City and Oreburgh City). Travel it all the way till you reach Spear Piller. After you have had battles with all of the Galactic goons you will face the Commarnders then the Galactic Boss. After that, Palkia or Diagla (Depending on your version) will be summoned and some animation will happen. After all of that, you will get a chance to save and heal then face the level 47 beast of a Pokemon.
These Pokemon helped you free Palkia/Diagla and now you can catch them. Each Pokemon is at a lake. Mespirt is found in the cave at Lake Verity. When you enter you can go talk to it and a picture of it will appear. Then it will run away. Rowen will come in and say some stuff and then leave. If you want to find it, you have to look on your marking map on your Poketech.
Azelf is in Lake Valor in between Hearthome City and Pastora City. When you go into the lake their is no more flopping Magikarp. Go into the cave and save it because this time you battle Azelf. Watch out for it's Nasty Plot move. It can be bad if your Pokemon aren't fully healed.
Uxie is in Lake Acuity near Snowypoint City. Go into the cave and fight a another non-running, Psychic Type Legendary. Uxie is different then Azelf because he is more defencive then offencive. If you can lower down his HP far enough he should be an easy capture.
Once you have the National Dex, go to the Island north of Sinnoh. Go to Stark Mountain and when you get there, a trainer will want to travel with you. When you reach a cave, he will take an item then run back. Go to the Survival Area and he will be in one of the Houses. Talk to him and he will run off. Go back to Stark Mountain and go to that little cavern you were in before. Save because you will have to fight the level 70 Beast called Heatran.
After you have transferred all the other Regis from R/S/E. Put them into your party and go to the Snowypoint Temple. You will be allowed access this time. When you reached the bottom level, solce the ice puzzles till you reach him. Save then you will battle the level 70 Regi King.
Come back later for more information.
After you have got the National Dex, go to Canalave City and under the Gym there will be a house with a sign next to it. Go into it and talk to the mum and son. Go out and talk to the sailor and he will take you to Full Moon Island. Follow the path till you can go into another part on the Island. In there it will have Cresslia. Talk to it and it will run off. Take the item it leaves and go back to Canalave and talk to the boy and mum. The boy will be better. Now you can search for it on you Marking Map Poketech app.
Manaphy is only obtanable from Pokemon Ranger. It will hatch from an egg that you sent over. You can breed the Manaphy only with a ditto. It will hatch into Phione, a weaker version of Manaphy.
Notes: For Giratina, I am making a little more information.
