Your Vacation is Over! Edit
Wario attempts to get the Mario Brothers to come back to the mushroom kingdom with him, but the Mario Brothers refuse to go with him. They are able to escape his lair by outsmarting Wario, but he vows to get them back.
Luigi stays with Wario Edit
When Mario goes too far with his bragging, Luigi decides to stay with Wario and eventually return to the Mushroom Kingdom with him. For some reason though, Wario never takes him back to the mushroom kingdom, and they stay at his house for a while. In the short time spent with Wario, Luigi wants to go do fun things that Mario and him would usually do, but Wario refuses, saying he'd rather stay inside his lair. Finally fed up with his constant activity suggestions, Wario tells Luigi to leave and go back to Mario saying, "I'll get you back later when I feel like it...weeah!".
Life at Wario's Lair Edit
Wario then spends time at his house watching bad movies like the golden compass. When Waluigi teams up with him, they use the lair to scheme, as well as hide when they steal from others, like when they stole Donkey Kong's Bananas
Lair abandoned Edit
Eventually, Wario's House dissapears from the series. The room used to film Wario's house becomes Mario's bedroom, so we never again see Wario's House. Wario and Waluigi just hang outside for the rest of the series... and considering many of the events of season 2 and 3 took over a year in the SMB universe... that means they went without living inside a house for a long time... It was never said why Wario abandoned his home. One possibilty is that after DK found him and Waluigi there, they realised it was not safe anymore and left. Another is the fact that since he was the villain in Season 3, the heroes could've started loooking for him in his house.
Lair Not abandoned AnymoreEdit
Wario has recently been seen in his lair in Act I Part 1 of The Stupid Mario Brothers Movie. It's only shown at the begining before Mario, Luigi and Wario start to dance! It is possible that now that DK and Wario are allies, it was safe for Wario to return.
Wario and Waluigi are seen discussing a time Wario encountered Roy from Fire Emblem. When Waluigi asks what happened to Roy, Wario says that Ike took his place (an in-joke to Super Smash Bros on how Roy got replaced in Brawl by Ike). They later have a singing competition which Waluigi wins after their DSs get stolen.