The Burnt Tower is a tower that first showed up in Generation II and is found in Ecruteak City. It is in the top left of Ecruteak City. It is only in Gold/Silver/Crystal and HeartGold/SoulSilver versions. When visiting this tower, you will encounter a mystery trainer named Eusine who is hunting for Suicune. Morty, the Ecruteak gym leader, will also be there. If you go into the basement, you will encounter Entei, Raikou, and Suicune. They will flee, however Suicune will pause and look at you momentarily first. After this, Suicune will be spotted in other areas in Johto and Kanto. Raikou and Entei will be roaming Johto, and can be randomly encountered in the wild.
In Generation IV the Burnt Tower shows up again in Heart Gold and Soul Silver and with more detail. First of all there's trainers you can battle in the Burnt Tower that have fire-type Pokémon and shouldn't be a threat if you come prepared. The next thing is that Burnt tower is much more difficult to move around in than Generation II because there's more boulders and rocks to move, but you can easily move them with the proper HM like Strength (For moving boulders) and Rock Smash (for breaking small rocks in the way). Usually each rock or boulder has a hidden treasure like an item after you move everything out of the way so be sure not to miss anything. Another thing in the Burnt Tower you'll see when you first walk in is the Gym leader of Ecruteak City, Morty. Morty is there because his friend Eusine is there tracking down Suicune and as you can see at the bottom of Burnt Tower is Entei, Suicune, and Raikou. When you try to go down there your Rival stops you and tells you that: "you're not strong enough to catch such powerful Pokémon", after that he battles you and if you beat him he'll just walk off. As soon as you get down there though Eusine comes and he scares the Legendary Beasts off enabling you to catch them for the first time. Overall the Burnt Tower is a must see place, whether you own a Generation II game or a Generation IV game it's important that you go there if you want to take the first step to catching the Legendary Beasts or just to sight see and look for items or trainers that you wish to find somewhere throughout the Burnt Tower.