I don't thik any of the legendaries should have a story. If they do, then a very minute one, more of a side-adventure than a must-complete, like in 2nd gen.
My ideas.
*Note: All legendaries are available forcapture MORE THAN ONCE. No one-of-a-kinds. EXCEPT Mewtwo. I only say this because Mewtwo is a clone and realistically, there only CAN be one--right?
For one: I think legendaries should be breedable with Ditto--anyone agree/disagree? Idk though-if they aren't one-of-a-kind's, then it doesn't matter.
Entei: Volcanoes should be littered across the map. In Kanto, you can only find Entei on Cinnabar Island, if you haven't yet encountered one. An erupting volcanoe signals you that an Entei is in that vicinity. Entei can be found even in dormant volcanoes, but is rarer, and does not appear as a sprite on the field (or whatever it is called; the area you walk around on haha). Entei can range from levels 3 to 40 (craaazy) when in a dormant volcanoe, but in an erupting one, the Entei causing the eruption is considerably stronger, and can be caught at levels 60-75. In some of the harder volcanic areas of the game, strong trainers may have an Entei in their roster.
Raiku: I like the battle idea between Raiku and Zapdos. Here's my own idea. During storms (another weather concept I thought of), Raiku can be found at the front of the storm, standing right on the edge of the cloud's shadow. Raiku leads the storm from one area to the next. Until you gain certain abilities or something, Raiku will always flee when he sees you approach (from the main map once again). Once you gain a certain ability or something like that, you can then approach Raiku, and challenge it to a battle. A Raiku will be leading every thunder storm in the game.
Fun-idea: If you have a party full of pokemon with the static ability or whatever (the one that paralyzes foes on contact), and you use enough of them in battle, whether they get k.o.'d or not, you may attract a Raiku with all the static. The magnet pokemon also appear frequently for a short time after. Note: Every time Raiku appears in the wild, a thunderstor is literally right behind him, or nearby. I think when battling, Raiku should also cause a thunderstorm to apper. It affects flying and water-types badly, and says something like "Fearow was damaged due to static in the air" or something like hat, and of course it powers up electric-based moves. Raiku in the front of storms is always at level 50, while raiku's around storms or in them are found at levels 5-40.
Suicune: This legendary is found very rarely at lakes/streams/rivers. NOT oceans. when suicune is in the area, local grass types have more health, and water types as well, and water types are a bit stronger. (This would also be a great way to raise/train pokemon, by catching them whilea suicune is around). The slightly altere pokemon stats are due to Suicune's presence "purifying" the water, therefore giving the surround plant and grass pokemon life more nurishment. Suicune is found at levels 5-50, probably depending on the area of the game. Also, in areas where grimer/muk usually appear, if a suicune is around, these pokemon will temporarily be unavailable, as in you won't see them, due to the pure water.
Note: Will NOT be found EVER in marsh areas.
Ho-oh: Ho-oh can only be found by leavig the rainbow wing in the burned tower, and then checking back every once in a while, to see if one has roosted there. I suppose in canyon-like areas, Ho-oh can be found resting in hard-to-reach places. Ho-oh appears at levels 30-60, depending on the area.
Lugia: Lugia is found maily at the whirl islands (or whatever it was called that you find him in in silver). Lugia is found at/near the place he originally was hiding, and also, the water in and around the caves is divable, so you can search for more canyons/Lugia's slumbering in the deep. If you come across a sleeping Lugia, you can still attack it as it slumbers, but it will wake up perhaps before one attack. When Lugia is in an aquatc environment, a whirlpool is formed and damages all pokemon excluding Lugia. However, the whirlpool disapears when Lugia is removed from battle.
Celebi: Available only in the same forest it is found in through Nintendo events, but no events are necessary. Celebi can appear at any given time, but rarely happens. You 'talk' to teh box it appears from, and it'll float down from the screen if it's around. If not... try again later. Celebi is found at level 30, and is recatchable. if you fail to catch it and it retreats (25% chance it will), it can appear in any forest in any region. Once you encounter one Celebi, others will be catchable at teh same spot, and in turn any forest that first Celebi visits. if you catch teh first celebi beforeit retreats, then other celebis won't appear anywehre except that one spot, until one retreats to other locations.
Mew: Found at the bottom of Lake Rage. The lake is now divable (only at the middle). Mew is VERY rare, and will appear as a sprite on the main map. Mew can avoid any ball besides the master ball (This may be farfetched). Mew appears atlevel 5 the first time you encounter it, and others are VERY rare afterwards, but can appear ANYWHERE, and always show as a sprite on the main map. They can appear in completely unaccessible areas (although won't happen much, but when it does, it's just to spite you), such as on top of a house's roof, or can appear in front of your house's door. Mew appears at levels3-15. Mew is the rarest pokemon. When you defeat the elite four for teh first time, Professor Birch explains a strange pokemon is sighted at the lake of rage. the dive spot is where the red garados used to be found.
Mewtwo: the only one-of-a-kind pokemon. this pokemon may have a story (not a huge one though). it's story is after breaking free from it's creators grasp, it was locked by Lance and the elite four in a dungeon until a trainer who was strong enough (proven by defeating it's captors) entered the dungeon, and attempted to catch it. The trainer used a very very strong team of pokemon, and was actually able to defeat Mewtwo. Mewtwo allowed itself to be captured, after seeing it' opponent was worthy. However, mewtwo longed to be free, so the trainer (Red) released it to the wild once more. Mewtwo, after roaming the lands for many years, returns to the Unknown Dungeon, and is trapped inside by Lance (who thinks he escaped). Once you defeat Lance, you are able to once again try to free mewtwo....by capturing it.
Fun-idea: Mewtwo is capturable with the master ball, but if youuse that, it wil take a VERY long time for him to start liking you. If you use a pokeball, he will submit fully to you and warm up to you very quickly. With increased catch-success rate, you lose respect from Mewtwo, and you gain time needed to earn it back.
Articuno: Can be found in harsh, extremely cold conditions, and only when you are about to black out (sorry I stole someone else's idea! If you thought of it, by all means, take credit where credit is due [here]!). FYI: Trainer 'blacks out' when he himself is exposed to conditions for too long. When he loses all party members,he 'whites out'. Articuno, no matter what, will return you to a Pokecenter. If you catch it, it will return you to a pokecenter to heal (the nearest one) and be stord. If you defeat it completely, you'll go to the map, but then text on the screenw will say "Articuno ate a berry" or something like that, and then Articuno will rescue you from a blackout. If it defeats you, then your character will wake up in a pokecenter (nearest one, once again), and you will have no idea how you got there (but that's any time your defeated). Articuno can also be found any where during a blizzard, but once again, only if you are about to 'black-out.'. Actually, Articuno should still be able 2 be found if not about to black out. Howeve, it's a VERY VERY rare find. Articuno can be found of course in the seafoam islands (I think I already mentioned that), and in a added-on room of Ice Path.
Zapdos: Can be found in highly magnetic/static areas and in teh eye of thunderstorms (which are lead by Raiku). You access Zapdos by using fly when you get to the eye of the storm (a slightly less chaotic/still rainy/stormy environment). It will show your character fly offscreen, but will then allow you to fly on another 'map' that is far off the ground, showing the landscape below as a silhoutte. You can travel freely. Then Zapdos flies to you (as an on-map sprite), and the match begins. Now, either A) You must have another flying pokemon/pokemon with levitate ability to fight Zapdos (due to the one your riding can't fight with you riding and non-flying/levitate types can't float/fly themselves), or the fight goes back to the ground. In any case, a thunderstorm invironment would be the battle scene here. Zapdos can be found at levels 5-60, depending on the Raiku leading the storm.
Moltres: Can be found in harsh, extremely hot/volcanic environments, and by using fly in windy areas (see idea I mentioned earlier...or ask me if you'd like me to explain again). Moltres can be found at levels 5-50. and...that's pretty much there is to it for this one...
Regirock: Is found at it's original spot at original level, but also found in Mount Moon in the same area/around the area where clefairies can be found dancing or whatever. Regirock is found at levels 30-50, and is quite rare. (As in rarer than most legendaries.) Regirock could also be the cause of the landslide event that I mentined earlier. also ask me about that
.
Regice: Found at original spot at original level, but can also VERY RARELY be found on Ice Path, and at the seafoam islands. At snowpoint, Regice can be found near the dock at Snowpoint during a blizzard (reasoning-blizzard + sea = lots of ice
).
Registeel: Found in original spot at original level. Also can be found inside Mount Coronet, Mount Silver, and the Unknown Dungeon (very rar here).
Fun-idea: About the 3rd Gen. Regi's, I think they should all be findable in the unknown ruins in Jhoto.
Latias: Found originally roosting in Bellsprout Tower from Jhoto. After approached, it flees. After you K.O./capture the first Latias, more become available in all regions, Hoenn especially.
Latios: Found originally roosting in Bellsprout Tower from Jhoto. After approached, it flees. After you K.O./capture the first Latios, more become available in all regions, Hoenn especially.
Kyogre: Can be found in original place at original level, and can also very very rarely be found roaming open ocean (as a sprite of course). Found at leves 5-40.
Groudon: Can be found in original place at original level, and can also very very rarely be found roaming the land NEAR volcanoes, as a sprite on the main map. Found at levels 5-40.
Rayquaza: Can NOT be found where it originally was. At levels 15-70, Rayquaza can be found using only the flying method I suggested earlier. Ask about it if you don't recall.
Jirachi: After you catch Celebi, go to the Onix Rock (forgot where it is exactly--anyways it's a memorial to an onix that supposedly died there and became a statue). If Celebi is first in your party, then Jirachi will appear, at level 5. After that encounter, as long as you have Celebi first in your party, Jiraci will appear around Onix Rock at levels 5-15. Why Onix rock? I don't know. Make up a story if you like! Or ask me to and I will
Deoxys: Found on a strange Meteor that crashlands after completing a certain event. The meteor crash lands on Mt. Moon, where the Clefairies dance.
Rotom: Can be found where originally found at the original level, and can also be found at levels 15-20 in Rock Tunnel, but with a catch. the HM Flash can't be used--you have to search for it in the dark, and after so long in the dark, your character 'black's out'. Rotom is kinda deep in the cave as well, like almost halfway through. Rotom can also be found at the other end of Rock Tunnel, in Lavender town at night, inside the local's TV's.
Uxie: Same as in-game, and same rules apply as Mew, but Uxie is slightly more common.
Mesprit: Same as in-game, and same rules apply as Mew, but Mesprit is slightly more common.
Azelf: Same as in-game, and same rules apply as Mew, but Azelf is slightly more common.
Note: The above three should be available in the unknown ruins of Sinnoh as well.
Dialga: Depending on the day, it will appear at night and early morning at the sky pillar. This is the only place and time it will appear, but you can return every other time the conditions are right, and catch another one, at levels 40-60, depending on your current party.
Palkia: Depending on the day, it will appear late in the evening at the sky pillar. This is the only place and time it will appear, but you can return every other time the conditions are right, and catch another one, at levels 40-60, depending on your current party.
Note: The days for the above.
Dialga: Monday, Wednesday, Friday
Palkia: Tuesday, Thursday, Saturday
Creselia: Found at the same place as in-game, but no event necessary. Also, can be found at the Spear Pillar on Sundays ONLY, in the evening, at level 5-50, randomly, and only after you have faced Dialga or Palkia. Here's how the level is determined:
Faced Dialga last: Randomly, level 5-24
Faced Palkia last: Randomly, level 25-50
Heatran: Born when a volcanoe erupts (due to Entei). Is ONLY a sprite on main-screen, and can be obtained shortly before an eruption by finding it's egg in the bottom/center of a volcanoe, or at level 5 when a volcanoe is erupting. Shortly after the end of an eruption, Heatran can be found at levels 10-15, but not for long, and soon becomes impossibe to find until the next eruption.
Regigigas (ALMOST DONE!!!): Can be found at Snowpoint Temple, with Regice, Regirock, and Registeel, acquired at in their respective temples, at level 60 (this is a oncer--at least at this location). Can also be found very rarely near the middle of Mount Silver.
Giratina: Turnback cave (no events necessary). Also, at the cemetary island in Hoenn, at level 80. Yea! Powerfu (Debatable, for sure)! I dont' necessaryily want it to be better than Mewtwo.
Phione: Available in the three great lakes of Sinnoh by diving. VERY rare. Just a smidge more common than mew. Can also be found in the area Mew is encountered in the lake of rage. Can occasionally be found just outside of pallet town--surf to Cinnabar!
Manaphy: Found in divable areas near seafoam islands, Snowpoint, and the whirl islands in Jhoto.
Darkrai: On Tuesdays only, can be found at the sight of the dancing Clefairies on Mt. Moon, and also at the top of Pokemon Tower in Lavender Town, where it will always be accompanied by a level 30 Marowak. Also found (once) on New Moon Island, at level 50.
Shayman: Same as in-game, but no event necessary. Also EXTREMELY rare in flowery fields, a bit more common near Valley Windworks.
Arceus: Found in the Hall of Origin. The Hall of Origin is accessed only after completing the main game and gaining access to Unknown Dungeon, where Mewtwo will be faught once more. You MUST capture Mewtwo in order to access Arceus (doing so with a Pokeball/Great ball is recomended, as Mewtwo will preform better the more it trust/respects/likes you). When you get to "wherever you go 2 find the hall in 4th gen.), Team Rocket accompanied by a team of scientists rush by in a group of helicopters. Mewtwo recognizes Lance, chasing the helicopters on DRAGONITE. Mewtwo gives chase, taking you with it, wishing to extract revenge on the one who imprisoned him. Note: Mewtwo is allowed out of his pokeball (like what I was talking about earlier for smaller pokemon...ask if you don't know about) specifically for this event (so obviously you need Mewtwo with you). When you reach the Hall (which is a encased in a stone prison, barred, gold doors blocking the gates), you find Lance defeated by the Rockets, behind the group, Giovanni emerges. He rambles on about how he's been in hiding, and researching about the one Pokemon capable of surpassing them all. He sets Dialga's and Palkia's orbs in to slots on the golden gates, and places the silver wing and rainbow wing (feather) in two slots as well. He also takes the items you get to summon Kyogre/Groudon and places them in slots along the doors. He then takes a specially made ball (the one required to be crafted in order to obtain Celebi), and places it in a middle slot. He then turns to you and Mewtwo and says how the profecy required one who surpassed the rarest of all (Mew) to pry the doors open. You then battle Giovanni (who has a VERY strong team). After defeat, he and the rockets/scientists SEEM to leave. Mewtwo then, acting of his own accord, pry's the gates open using telekinesis. Lance (who was previously defeated by Giovanni) states that Mewtwo seems to be throwing a gelous anddangerous rage. Basically--Mewtwo vs. Arceus. Creation vs. Creator. Arceus is NOT catchable during this battle. As Mewtwo ALONE, you must defeat Arceus without items. give him a good power-up before the confrontation. the reason it's just mewtwo is because the main cahracter isn't controlling him, he is acting by himself (it's just you get to play it out). After Mewtwo defeats Arceus, Arceus fleas, and Giovanni is convinced the legends about Arceus musn't be true, if Mewtwo was able to defeat it. Arceus then acts like the legendary dogs, fleeing across the countryside. Arceus can be caught more than once. How? the scientists enter the Hall of Origin, and extract Arceus DNA... Same as with Mew... >:] NOT saying an Arceustwo should be created. BUT this plot DOES kinda make it practical, does it not? Anyways, more arceus' become available due to new cloning by the scientists.
and there you go. My legendary-encounters list. Sorr that it was sooo ****ing long!
edit: I realised Arceus contradicts with the fisrt thing I said--legendaries shouldn't have a major story. However, I feel that this is epic in a sense that it would work out. After all,it is NOT the trainer that is fighting said "god". :l No need for god. that's why I have mewtwo prove the legend wrong
Your's was great firusthehedghod 
