The bunker is located in Polis, which would have been Baltimore area (Maryland, US) before the first nuclear apocalypse. It's large enough to support 1,200 people for five years.
The bunker has six levels, labeled A through F. Level C contains the hydrofarm and the water recycler, which are completely self sustainable should the rest of the bunker fail. The cafeteria is also located on that level. Level D contains the generator. The bunker also includes underground aquifer with a filtration system, oxygen and air scrubbers, medical area, and airlocks. Supplies left behind include hazmat suits.
The Second Dawn cult decorated the bunker with signs, flags, and posters with their logo and adages. Near the entrance, there is a flag that reads "From the ashes, we will rise." The cafeteria includes posters with quotes "blood must have blood" and "your fight is over". All three Second Dawn adages became important Grounder sayings.
When the bunker was controlled by the Second Dawn, it had a room that was used by Bill Cadogan as his lab. When Wonkru took control of the bunker, this room was changed into a rec room. In both instances, the room contained a piano and the Anomaly Stone, though the Stone was buried in the floor during Wonkru's reign.
The bunker was built sometime before the Nuclear Apocalypse by the doomsday cult Second Dawn which was led by Bill Cadogan. When the Nuclear Apocalypse occurred, 1,104 people made it into the bunker, 92% of the Level 12's slated to live there. It held the Second Dawn for two years before the cult split, one faction led by Callie Cadogan leaving to return to the surface using Becca Franko's Nightblood while the rest became the Disciples and left Earth for Bardo through the Temporal Anomaly. At some point later, the Anomaly Stone was buried in the bunker's floor, presumably by Azgeda as an Azgeda symbol was burned into the floor over the Stone's burial site.
According to Gaia, Becca is buried in the bunker, implying that her ashes are kept in there after she was burned alive at the stake, but A.L.I.E. 2.0 managed to "crawl out of the flames", like it said in the notebook. The Flamekeepers came to believe that the phrase "salvation lies within" referred to the Polaris escape pod that Becca had come to Earth in which was positioned over the bunker entrance.
According to Thelonious Jaha, while he knew of the possibility of the bunker's existence, he didn't consider it for the Delinquents to use when they arrived on Earth as its existence couldn't be proven.
With the approach of the Second Nuclear Apocalypse, Jaha sought out the bunker as a possible means of survival, eventually locating it long-since abandoned beneath Polis. The bunker became the home of Wonkru for six years during which time they were trapped underground by the collapsed Polis tower. The bunker was eventually freed by the Eligius prisoners and remained the home of Wonkru until the clan marched on Shallow Valley following the destruction of the bunker's hydrofarm by Octavia Blake in order to force Wonkru to follow her to the valley.
125 years later, Clarke and her friends return to the bunker and the regenerated Earth during their conflict with the Disciples, the descendants of the cult that had originally built the bunker. The group decides to live in the bunker again until they can build their own shelter on the planet's surface. The bunker is severely damaged when the Disciples send a bomb through the Anomaly. Though the airlock contains the blast, both the airlock and at least one corridor collapse as a result. However, the Anomaly Stone is rediscovered by Raven Reyes, Eric Jackson and John Murphy, providing them with a way out while most of the rest of the group remain trapped elsewhere in the bunker.
In The Other Side, the bunker becomes over populated with approximately 1,564 people.
In The Chosen, Kane and Jaha gas their area of the bunker and sacrifice 364 Sky People in order for there to be enough oxygen and food for everyone else in the bunker as to make room for everyone.
In Praimfaya, Octavia, with Bellamy's and Indra's encouragement, takes the lead of the people within the bunker.
In flashbacks shown in Red Queen, Kara Cooper stages a coup to take the bunker for Skaikru. She locks the majority of Skaikru in level C, which includes the cafeteria, hydrofarm, and water recycler. Boudalankru took levels E and F, Oskejonkru took medical, and five different clans were fighting in level D. The coup changes Octavia's rule. She forces those who committed crimes, even minor ones, to compete in gladiator-style fights to the death.
In Pandora's Box, Octavia as an absolute leader of the bunker throws Kane in the ring in suspicion of stealing drugs meant to treat Wonkru. At first, she puts Kane weak opponents to make it easy for Kane to win. During the next match, Kane refuses to fight. So, Octavia is forced to go in and kill him herself. Just before killing Kane, the light comes through the roof of the bunker. Bellamy and Clarke are going down on the ropes. Bellamy had made a deal with Diyoza so that her prisoners can help open the bunker. Diyoza forces Abby to come with her because they need a doctor. Kane comes with them to avoid his execution by Octavia. When one of Diyoza's people goes against the orders and tries to attack Wonkru, Octavia declares war against the prisoners.
In Acceptable Losses, Clarke and Bellamy discover that Octavia and Kara Cooper have been experimenting on the parasite worms to use them as weapons against Diyoza and her people at the valley. They work with Indra to advise Octavia against it but she refuses and says that this is war.
In How We Get to Peace, Clarke and Bellamy come up with a plan to force Octavia to surrender by destroying her weapons - the worms. They attack Cooper with the worms to make it look like an accident before killing all the worms. Octavia easily figures out what they did. She reveals that the plan was never for them to use the worms. They were planning to use the worms' eggs. She orders for Clarke to be arrested for execution.
In Sic Semper Tyrannis, Indra tries to convince Wonkru to accept her as the new leader while Octavia is unconscious (after being poisoned by Bellamy). However, Wonkru rejects Indra due to their loyalty to Octavia. So, Bellamy and Indra devise a new plan to make Madi the new Commander because the Grounders would listen to her since she's a true Nightblood. While the ceremony is going on, Indra goes to check in on Octavia. Octavia wakes up and mentions that Bellamy poisoned her only to be shocked to on realizing that Indra was working with Bellamy. She calls out Indra for committing treason and for being a coward.
Clarke and Octavia convince each other that they are on the same side since they both don't want Madi to become Commander. They make a deal for Clarke to help stop Madi's ascension and for Octavia to help Clarke and Madi escape. Octavia stops the ceremony and orders for Bellamy, Indra and Gaia to be arrested for treason. She throws them in the ring to fight to the death.
In The Warriors Will, Octavia is in a dilemma because she doesn't want to kill Bellamy but at the same time, she wants to regain Wonkru's loyalty by throwing the traitors into the arena. Realizing that Indra is the main threat, Octavia tries to use Monty to send message to Bellamy, informing him of Indra's weaknesses so that he can win but Monty refuses and instead shows her that he's been working on the hydrofarm and it's almost ready to grow crops.
The fight begins, but before anyone dies, Monty and Harper interrupt. Monty reveals that the hydrofarm is working again, by using the same techniques. He tells them that they don't have to go fight for the valley. They have a choice to stay behind and use the hydrofarm. As Wonkru start turning against her, Octavia quietly goes to the hydrofarm and sets it on fire as a retaliation, leaving them with no choice. She then starts marching towards the valley. They all follow her, abandoning bunker.
In What You Take With You, while under the influence of red sun toxin, Octavia hallucinates herself in the bunker's fighting pit, chained down in the middle of the floor. Octavia is confronted by a hallucination of Charles Pike for her actions, both in the bunker and outside of it. Octavia admits that she wants redemption for her actions, but is interrupted by a manifestation of her dark side as Blodreina who demands that Octavia kill Pike again. When Octavia refuses, Blodreina prepares to execute Pike herself, but Octavia recognizes the speech Blodreina gives as the same Pike gave when he executed Lincoln. Octavia saves Pike who disappears and Octavia and Blodreina battle in the middle of the arena. Octavia manages to kill the manifestation of her dark side, declaring herself to be "Blodreina no more." She then wakes up in the Verge on Sanctum.
In False Gods, Raven asks Indra to get her 4 Wonkru welders from the bunker's maintenance team to help her fix Sanctum's nuclear reactor.
In Nakara, Nathan Miller and Niylah discover a cloth containing a symbol that they recognize from the bunker as being that of the Second Dawn cult. The two are confused about the connection it implies between the Second Dawn and the Disciples. At the same time, on Sanctum, while convincing Indra to take control of Wonkru, John Murphy and Emori point out that she was the true power behind Wonkru while they were in the bunker, keeping things going while Octavia was busy being Blodreina.
In flashbacks, as the Nuclear Apocalypse starts, Cadogan brings his family to the bunker. The Second Dawn is forced to seal the hatch early as a nuclear missile destroys Baltimore, leaving the bunker with 1,104 people, 92% of the Level 12's that were expected to make it. Cadogan refuses to allow the bunker to be opened for a year even with Hazmat suits, dooming people trapped outside of the hatch even as they desperately call for help. In the meantime, Cadogan works on the Anomaly Stone he recovered in Machu Pichu in order to bring his people to a new world while 20 people commit suicide and the rest start worshipping Cadogan for saving them.
Two years later, as ground teams scavenge through Polis, Becca Franko arrives. Cadogan has the bunker locked down so that no one will know she is there and Becca is drawn to the Stone. Using the Flame, Becca is able to open the Temporal Anomaly to Bardo, but argues for using Nightblood to return to the surface instead of going through the wormhole. With her father refusing to listen, Callie Cadogan begins recruiting people, getting half of the kids in the bunker and some of their parents. However, Becca discovers "the final code" leading to Judgment Day, the end of the human race. With Becca unwilling to give it up, Cadogan has her imprisoned and then burned at the stake in order to get the Flame for himself.
In the aftermath of Becca's execution, the survivors in the bunker split. Stealing the Flame, Callie leads her group back to the surface to save the remainder of humanity, bringing with them enough Nighblood doses for 2,000 more people. Cadogan exiles his ex-wife Grace for helping in their escape while Reese and Tristan, both Nightbloods themselves, chase after Callie to get the AI back. Cadogan and his remaining people, now going by the Disciples, abandon the bunker to travel through the Anomaly to Bardo.
In A Sort of Homecoming, Clarke, Raven Reyes, Eric Jackson, John Murphy, Emori, Indra, Octavia Blake, Gabriel Santiago and Cadogan emerge from the Anomaly in the bunker's fighting pit. Using nanotracking technology, Cadogan escapes back to Bardo while the group is greeted by Gaia. Gaia reveals that when a Disciple abducted her through the Anomaly, they arrived in the bunker where Gaia killed the Disciple. Gaia reveals that Nathan Miller, Niylah, Jordan Green, Echo and Hope Diyoza had all arrived that morning and leads the group outside onto the regenerated Earth where their friends have set up camp nearby. Feeling that everyone that she cares about that is left is on Earth, Clarke smashes the Disciple helmet that could lead them to the Anomaly Stone and decides that they will settle on Earth.
The group inhabits the bunker once again until they can build a more permanent home on the surface. With the Earth now habitable once more, Murphy and Emori press Raven to fix the Disciple helmet so that they can bring the Sanctumites, Wonkru and the Eligius Prisoners to the much-safer Earth. However, Sheidheda invades the bunker and kills Gabriel to get at Madi. Raven tries to use the helmet left behind by Sheidheda to track down the Anomaly Stone, but the helmet is damaged and unable to pinpoint its location. After Madi travels to Bardo, the Disciples send a bomb through the Anomaly. Miller contains the blast by throwing the bomb into the airlock, but the explosion apparently makes the bunker unstable as part of it begins collapsing.
In The Dying of the Light, Clarke, Octavia, Gaia, Miller, Jordan and Hope are trapped in the fighting pit by the explosion which has collapsed the airlock. Clarke and Octavia take the nanotracker pills left behind by Sheidheda and are eventually pulled to Bardo thanks to the efforts of Levitt, leaving the others behind. Echo and Niylah are nowhere to be found, having been in a different part of the bunker when the bomb went off.
At the same time, Murphy suffers a likely concussion in a corridor collapse, but Emori suffers an injured leg and impalement by a piece of rebar. With Jackson unable to save Emori on Earth, the group begins searching the rec room for the missing Anomaly Stone in the hopes of getting Emori to Sanctum in time to save her life. Murphy and Raven discover an Azgeda symbol burned into the floor, suggesting that the Ice Nation had something to do with the disappearance of the Anomaly Stone and begin excavating the spot with sledgehammers. As Emori's heart stops and Jackson performs CPR, Raven and Murphy uncover the buried Anomaly Stone. Using the Disciple helmet, Raven enters the code for Sanctum, causing the Stone to shoot into the air and hover over the floor once again. The Anomaly opens nearby and with Emori's life on the line, Raven, Murphy and Jackson rush her through it on a gurney.
Wonkru inhabited the bunker for six years after the second Praimfaya. Below list only includes members who lived in the bunker during the six years it was sealed.
In "Praimfaya", Indra says there are 1,200 inhabitants within the bunker. By "Pandora's Box", there is only 814. After the bunker is opened, they start using the space above ground as well as the bunker. Some the inhabitants also defect to Shallow Valley or are killed. After The Warriors Will, Wonkru left the bunker to march onto Shallow Valley, leaving the bunker uninhabited.
Several people were on Clarke's list or were seen in the bunker at the end of season 4 but have not been seen in season 5. They may have died at some point though their deaths are currently unconfirmed.
Out of characters introduced in seasons 1-4, Raven Reyes is the only character to survive season 5 who hasn't been in the bunker. Many characters introduced in season 5, including Miles Shaw, most Eligius prisoners, and Jordan Green, have also not been in the bunker. Raven and Jordan would later visit in Season Seven.
In "The Dying of the Light," its revealed that the Anomaly Stone was buried in the floor of Cadogan's lab which later became the rec room during Wonkru's time in the bunker. An Azgeda symbol burned into the floor over the spot suggests that they were responsible, though when, how or why they did it is unknown.