There are four ways to enter and exit the Cave. The first is the front entrance located at the base of Mount Justice, leading into the forest. The second is the back entrance that faces the Rhode Island coast, and the third is through the bay door in the hangar which opens onto the Atlantic Ocean. The fourth method is via one of the Zeta-Beam teleporter tubes, through which members of the Justice League and the Team can travel to and from various locations.
Other features include:
Grotto:A place of contemplation that had been there since the League's days, it became a memorial after Jason Todd's death. Holographic effigies of other fallen members of the League and Team were placed there too.
Hangar: The largest room is the multi-level hangar which contains two more Zeta-Tubes and the Cave's main generator.
Kitchen: A fully stocked open kitchen and eating area.
Library: A two-level library with reading tables and dozens of bookshelves. A secret passage was hidden behind one case.
Living quarters: A number of rooms, fairly similar in design, along a corridor.Superboy and Miss Martian were the first inhabitants after its reinstatement, though several others later moved in as well.
Locker rooms: Rooms to change, located between the workout room and the showers. Includes benches and lockers.
Lounge: Located in the same room as the kitchen, a lounge area with a couch and a large television.
Medical bay: To treat injured members. Contains advanced medical equipment, including a MRI scan and X-ray.
Mission Room: The central chamber, with a holographic computer. It can also serve as a training area. The Mission Room also has two Zeta-Tubes.
Red Tornado's apartment: In 2010, Red Tornado had an apartment above the Mission Room, where he kept his things and worked on his own projects. It was accessible through a hatch in the Mission Room's ceiling.
Showers: Used by members when they return from a mission and require sanitation, located next to the locker rooms.
A G-Gnome had sneaked into the mountain in the hope of being reunited with Superboy. Due to a psychic overload, the G-Gnome forced Superboy to relive Joker's attack on the Secret Sanctuary years earlier.
Red Inferno and Red Torpedo attacked the Cave, and captured Aqualad, Miss Martian, Kid Flash and Superboy. Robin and Artemis had to evade the Reds and come up with a plan; eventually, they made an EMP device on Kid Flash's instructions. After the Reds were defeated, Red Tornado returned, and sucked the air out of the Team's lungs. He made it appear like he had turned on them to keep them safe.
The Justice League checked in on the Team, and made sure they were unharmed. After Aqualad's conversation with Batman concerning a possible mole was overheard by Superboy, a fight nearly broke out between them. Batman tries to calm them down by giving them another mission.
Because the League did not give them any results about the search for Red Tornado, the Team decided the do their own investigation. They escaped the watch of the den-mothers Black Canary, Zatara and Captain Marvel while pretending to show around guest Zatanna, and then kidnap her.
Martian Manhunter lead a telepathic training exercise. Unfortunately, it went wrong when, in extreme emotional stress, Miss Martian took over command. Artemis, who had "died" in the simulation, slipped in a coma, and Martian Manhunter had to travel into the exercise to stop it. Afterwards, Miss Martian was devastated her powers had caused so much emotional damage.
Klarion's spell divided the world in two dimensions: one for adults and one for children. After seeing the other disappear before their eyes, both the Team and the League used the Cave as a base to coordinate rescue effort, and they formed a plan to stop Klarion by using Captain Marvel as a messenger between the dimensions.
Superboy, Miss Martian and Zatanna stayed behind. They soon got bored, and asked Red Tornado for a mission. But since there wasn't any, he left them to their own affairs. When he temporarily left the mountain, the three checked out his apartment, and found the John Smith android. Red Tornado was displeased at the invasion of privacy, but explained his intentions with the android to them.
With the rest of the Team on a mission, Wally prepared himself a late night snack. Robin contacted him, and Wally confronted him with the fact that the "mission" he was on was not one of Batman's, but one of his own. Dick opened up about the real reason, protecting Haly's Circus.
After capturing Riddler, Mammoth and Shimmer, and retrieving a case full of the Light's Starro-tech, Batman congratulated the Team, though he also berated them for hacking League computers and endangering their lives again. After explaining the mole matter to new member Rocket, Superboy, Artemis and Miss Martian revealed that they were being blackmailed by members of the Light.
Returning to the mountain after dealing the Light a decisive blow, the Team was told by Batman the mole in the Team was Red Arrow. They had a hard time believing it. The moment Batman left the Cave, Red Tornado powered down. Aqualad decided to split the Team up: he would search for Red Arrow, while Robin would work on Red Tornado in the Cave. At Zatanna's suggestion, they transferred Red Tornado's consciousness into the John Smith android. After Black Canary attacked them without provocation, Tornado told them to abandon the Cave. They left in the Super-Cycle.
Nightwing was working on the translation of the Krolotean intel they got from Malina Island, with Robin and Beast Boy standing by. They were surprised by the arrival of Impulse in a time machine. After a chase through the whole Cave, he was captured by Nightwing, but escaped when the door was opened.
Mount Justice February 28, post-13:03EST
After Impulse had helped defeat Neutron in Central City, the entire Flash family came to wave him goodbye, as he wanted to go back to his own time. The time machine did not work, and Impulse was stuck.
Impulse inadvertedly brought a trojan horse tracking device that wirelessly bypassed security systems. This allowed Aqualad's Team to infiltrate the Cave, incapacitate Wolf, Sphere, Nightwing, and Superboy, and capture Blue Beetle, Impulse, and Beast Boy. Aqualad also planted a bomb which he placed in the Mission Room. Once at a safe distance, they blew up Mount Justice.