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.
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 convinces 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 interrupts. 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 behind, abandoning bunker.
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.