Under the Railroad Tracks
Bowser's Hideout is where Bowser stays when he is warped into the real world by Nox Decious. It is a sinister cave located under the railroad tracks. The only ones that know of it's location are Wario, Johnny Cyclops, and Kamek.
When Nox Decious was plotting to rule the world, he created a portal in the cave underneath the railroad tracks so that Bowser, as well as his Koopa minions, could transport from The Mushroom Kingdom to The Real World with ease.
Wario chats with his MasterEdit
The Quest for the HiltEdit
Johnny Cyclops takes Link and Ness to Bowser's Hideout when they are searching for the Hilt, the second of the Nether Emblems. Bowser is not in the cave at the time so Link easily retrieved the Hilt from inside.
After the defeat of Decious, Bowser remained in the Mushroom Kingdom until he found a way to stop the Mario Brothers in the Real World. Once Kamek perfected a spell that can make Koopas appear human, Bowser came out ready to get the Mario Bros. Later on in Act II Part 2, Bowser and Kamek leave the Real World after unsuccessfully fighting Mario and Luigi going through a portal in the hideout.
Operation: Blind StormEdit
In Operation: Blind Storm Mario, Luigi, Wario, Solid Snake and Ness arrive at the hideout it apparently containing an Energy Source which Snake ends up destroying resulting in all characters losing their powers in the real world.