Real Life Legendary Locations

[Sequoia]

Mewtwo-Area 51. I know it's supposed to be aliens but its the only "secret" sinister sort-of lab I could think of.

Going with what Charlie said, I think Deoxys would be found at Area 51, not Mewtwo.

I have to agree with Roko, Deoxys makes a bit more sense. Perhaps Mewtwo can be found in that cave with the gigantic crystals in Middle/South America (the name escapes me at the moment). In the Kanto games, it could be found in Celadon Cave, and the crystal cave has such high temperature extremes that it can be assured that only the hardiest trainers with the best pokemon (and at least one ice type) would even try to go down there.

Mew could be on a bridge somewhere.

What, you mean like the Brooklyn Bridge or something?

[Noah_Road]

I can see Dialga, Palkia, and Giratina in their own dimension that connects to our world through 3 special places.

Dialga's portal or link to our world could be located at Big Ben in London since they both are so well known for time.

Palkia's link could be somewhere in Tokyo since they are so dense in space--something that represents the legendary space pokemon.

Giratina's link would probably just be anywhere since I can see him choosing where he wants to open up his portal (and I can't think of a good place in the world xD)

I can see Jirachi's home being on Haley's Commet itself and it only comes to earth when the commet is close to earth.

Heatran would probably be living in the earths core.

[Roko]

I like the Jirachi idea. Hayley's commet can only be seen once every 77 (I think) years, and Jirachi supposedly appears once every 1000 years. So it's linked... not closely, but hey!

[Noah_Road]

Yeah true but maybe in our world Jirachi could visit ever 75 years instead of every 1000 lol. Its easier than finding a commet that comes every 1000 years xD

[TrainerX]

 Mew could be at Akashi Kaykio bridge.

[Noah_Road]

I thought Mew never really stood still. Plus its pokedex info in gen 1 said that it was last seen in South America....I think.

[Roko]

Yeah, but the only way to get Mew in the old games was the Mew glitch, and it was found on the Cerulian Bridge, which is why they're going for bridge ideas.
Also, I remember that Mew could be found in jungles in Pokémon Ranger.

[TrainerX]

 The South American thing could work. Maybe in the amazon?

[Sequoia]

We originally had Celebi in the Amazon, but I think Mew might indeed work better. Perhaps Celebi  could be in the Black Forest. Or how about a bamboo forest in China?

I can see Dialga, Palkia, and Giratina in their own dimension that connects to our world through 3 special places.

Dialga's portal or link to our world could be located at Big Ben in London since they both are so well known for time.

Palkia's link could be somewhere in Tokyo since they are so dense in space--something that represents the legendary space pokemon.

Giratina's link would probably just be anywhere since I can see him choosing where he wants to open up his portal (and I can't think of a good place in the world xD)

Now that's an awesome idea.  Thinking of where Giratina's portal would be, the first place I can think of would be...Chernobyl? 

[Noah_Road]

Maybe Giratina could be held at Alcatraz! Since its an "evil" pokemon, and we humans needed a way to seal it, maybe we locked it up in one of the most famous prisons ever! I can picture a chained up Giratina in an enourmous holding cell.

[Roko]

I like the Alcatraz idea. An abandoned jail is the perfect setting for a portal to another dimmension!

[TrainerX]

 Alcatraz could work. Or maybe he could be in this one place where this guy claims to have traveled through time. He believes he went through some kind of portal, which led to half an hour in the future. I don't remember where it was though.

[Noah_Road]

Wouldn't a place like that be more of Dialga's kinda habitat?

[TrainerX]

 But he claims he went through a portal, and was in a another dimension where time flows faster, so that's why I thought Giritina could be there.

[Noah_Road]

Ohhh I get it. What about Zekrom and Reshiram? I can see Reshiram residing in Mt. St. Helan while Zekrom hangs around Mt. Rushmore.

And then what about Terrakion, Virizion, and Colbalion (and to some extent, Keldeo)? Since they are based of the 3 musketeers maybe they would reside in Paris. Since they are sworn to fight humans for the sake of pokemon I can see them roaming the streets secretly in central Paris because they are wanted for hurting people.