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In Pokémon Silver and Gold, Lugia is meant by many to be the strongest because of its amazing powers in all fields. It's also just the right level once you get Whirlpool (and Silver Wing...)

Ho-Oh is a legendary that lots of people miss (or that's what it seems to me) because of Lugia's great survivability, but it's still a pretty great Pokémon!

Mewtwo is a Pokémon it requires a lot of patience to catch (it's going to be hard to wait with your masterball for 40+ levels...), but it's simply the single most uber Pokémon. Truthfully, I've never had it (not the patience, plus I was like 6 when I met it...).

The dogs are cool, and decently strong as well, but you should really just go for Lugia and Mewtwo. Both of them. Mewtwo because it's so strong, and Lugia because it's so strong and extremely cool (I mean have you seen the movie?).

The three birds aren't very important. Still, you'll need 'em for the dex, so why not catch them anyway?

So, get Lugia and Mewtwo. Both are psychic, sure, but that's a cool class anyway, right?

Oh yeah, Celebi. I've never had this Pokémon either, but it's a legendary grass-type Pokémon, right? That's rare. In fact so rare it's the only one except Shaymin (but that's not until P/D/Pl (or is Regigias grass?).

If you've got SoulSilver and HeartGold, Arceus is sweet, and so is Giratina. Palkia and Dialga are okay, but the two others just rock. Don't forget Darkrai!

There's also Jirachi of course, never had that one, and I know nothing about it. Except that it makes wishes come true or something. Still, I've never had a million Masterballs in my bag, so don't count too much on it.

There are the regis, but catch them for the dex, not the party.

So... get all the legendaries, but aim for Lugia, Mewtwo, Arceus, Giratina and Darkrai. In that order as well. Or switch Mewtwo and Lugia, whatever you want. You might want to switch the P/D/Pl Pokémon a bit around as well, but I don't know anything about these new Pokémon (not too much anyhow).

Have fun, stay safe!

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Q: What is the strongest Pokemon in Pokemon Silver?
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