It was first seen in "Finding Mr. Right" when Robin was sulking in the cave after he was unsuccessful in making Harley Quinn his nemesis and Batman gave him a grilled cheese and opened up about not having a nemesis himself until his twenties.
In "You're a Damn Good Cop, Jim Gordon" Harley Quinn stole a device from WayneTech in the form of a button which transported her into the Batcave when she pressed it. There she got stuck on a rock, almost falling to her death but she managed to convince Batman to save her and take her back to the Gotham City Police Department to be a better friend to Jim Gordon.
In "Batman's Back Man" after waking up from a months long coma, Batman has a meeting in the Batcave with Lucius Fox who presents him with a new high-tech suit as Batman wants to get back into crime fighting again. Although, Alfred takes the suit to his room, insisting he isn't well enough to be Batman again.
Despite still being recovering, Batman spend his time in the Batcave and uses it to pilot the batplane with Gordon in it during "Dye Hard". Later, in "A Fight Worth Fighting For" he is agains seen there, still using it as his base of surveillance which is how he finds out about the Joker's return. It is also then and there that he decides that he is finally ready to go back out on the streets again.