With the death wave approaching, the Grounders and Sky People decided that control of the Second Dawn Bunker would be decided by a Final Conclave. Octavia Blake won the Conclave but instead of just leading Skaikru into the bunker, she decided that the remaining clans would form into a single clan, known as "Wonkru" ("One Clan" in Trigedasleng), and share the bunker equally. Thus, 100 members from each surviving clan (excluding Floukru, who all had died) were ushered into the bunker to survive.
At first, Octavia ruled over Wonkru as Osleya (Champion in Trigedasleng) with a council consisting of a delegate from each of the clans. However, after nearly two months of relative (albeit tense) quiet, part of Skaikru led by Kara Cooper rebelled against Octavia and barricaded themselves inside the bunker's cafeteria, isolating the rest of the people from their food source. This led to massive chaos in the rest of the bunker. Octavia, advised by Thelonious Jaha, reinforced the union of the clans by killing those who dared oppose her.
After the rebellion was thwarted, Octavia took full control of Wonkru and became known as Blodreina ("Red Queen" in Trigedasleng). Anyone who committed any crime was considered an enemy of Wonkru. Justice was then served via gladiatorial fights to the death, with the winner possibly earning their freedom.
About two years after Praimfaya, a fungus devastated the soybean plants. Cooper was able to isolate a few healthy plants but said that it would take a year before the farm would recover enough to support the bunker's population. Without a proper source of protein, people would die of malnutrition, so Abby Griffin proposed a grim solution: Eating those that died in the fighting pits. However, in the mess hall, Marcus Kane tells everyone that they have a choice not to eat. Afterwards, Abby tells Octavia that to survive they must have full compliance, citing the Blight Generation on the Ark to describe what happens if they don't. To gain said compliance, they must make refusing to eat a crime. At first, Octavia objects to killing her own people, but then grudgingly agrees with Abby that there is no other choice. The next time people refuse to eat, Octavia begins to kill three of them, until Kane and the other resistors agreed to eat. Wonkru calls this year of cannibalism – their second overall year in the bunker – "The Dark Year", named for the serious emotional repercussions left on Wonkru as a whole.
During the six years in the bunker, the population was reduced from approximately 1,200 people to 814. In other words, approximately 386 people died during those six years of Octavia's rule.
Six years after Praimfaya, the Eligius prisoners open the bunker after making a deal with Bellamy Blake. The prisoners lift everyone out of the bunker, but then betray the group by claiming the Shallow Valley as their own and demanding Abby Griffin because they need a doctor. Abby agrees to come willing if they take Marcus Kane as well, since Octavia is holding him prisoner to fight in the gladiatorial matches. After the prisoners leave, Wonkru declares war on them, thus starting the Battle for Eden.
Octavia sets out across the desert with a battalion of soldiers, but parasitic worms and a sandstorm hamper their progress towards the valley. Monty warns them of incoming missiles, and later that night, the Gagarin fires a missile at the Wonkru campsite. However the campsite is empty, since the battalion retreated into the sandstorm. Between the worms and sandstorm, Wonkru returns to Polis with twelve dead.
Later, the Gagarin drops food supplies and a message in Polis. Diyoza tells Wonkru that they can defect from Octavia's leadership and join her at Shallow Valley. Octavia sends Echo to infiltrate the Eligius camp to get access to the ship's computer by posing as a Wonkru defector. That evening, several real defectors join Echo to escape Polis and board the Gagarin. However, Kara Cooper, on Octavia's orders, shots at the defectors, killing several of them.
Within the bunker, Octavia and Cooper begin experimenting with the parasitic worms. They hope to use the worms as bio-weapons against the prisoners in the valley. Cooper, without telling Octavia, infects a surviving defector to study the effect on a live body. Clarke, Bellamy, and Indra sabotage the plans by using the worms to kill Cooper and destroying the worms. However, Octavia sees through the ruse and has Clarke arrested for Cooper's murder.
To prevent Clarke's execution, Bellamy puts Octavia in a coma to prevent her from executing Clarke. Bellamy and Indra plan to have Madi take the Flame so she can become the Commander of Wonkru. Octavia awakens but Indra locks her away, while Gaia successfully inserts the Flame. However, before the ascension ceremony can be completed, Clarke releases Octavia. Octavia has Gaia, Indra, and Bellamy arrested, while Clarke and Madi escape in the rover.
Gaia, Indra, and Bellamy are forced to fight in the arena, but Monty and Harper interrupt. Monty reveals that the hydrofarm is working again and they don't need the valley. After Wonkru begins to rebel against her, Octavia burns down the farm, leaving them no choice but to march with her towards the valley.
During their travels, Echo contacted Bellamy with intelligence on the Eligius prisoners' battle plans. Bellamy offers Octavia the information if she agrees to his terms: to accept the prisoners' surrender with no executions or fighting pits, but real peace. Octavia agrees and the two plan for battle.
Four days later, the Wonkru soldiers enter a gorge at the edge of the valley. However, the prisoners are ready and massacre them. Unbeknownst to Wonkru, Kane and Diyoza, who had been with Echo, revealed Wonkru's plans to McCreary. Some Wonkru survivors are able to retreat back to their desert campsite, and Madi with three others rescue Octavia, Bellamy, Indra, and Gaia.
Back in the desert, Octavia relinquishes control of Wonkru to Madi, allowing her to officially become the Commander of Wonkru. The Flame helps Madi create a plan and they successfully invade the valley. The prisoners surrender, and Bellamy convinces Madi not to kill them and to break the cycle of deaths. However, McCreary refuses to surrender and deploys the Damocles bomb, before he is killed by Clarke. Everyone is forced to flee onto the Gagarin to escape to space and the bomb destroys the valley.
In space, they board Eligius IV and decide to go into cryosleep for ten years while Earth recovers. However, Earth remains barren, so Monty Green extends the cryosleep while he searches for a solution. After 125 years in cryosleep, Wonkru arrives to a new habitable world.
In "Praimfaya", when the bunker is sealed, there are 1,200 living members of Wonkru.
By "Pandora's Box", there are only 814 members of Wonkru remaining. Abby and Kane's decision to get into Charmaine Diyoza's ship peacefully makes them enemies of Wonkru, and twelve other members die in "Shifting Sands", leaving 800.
In "Exit Wounds", Octavia makes Madi a member of Wonkru, but an unknown number of defectors manage to reach the Gagarin transport ship, and others are killed by Kara Cooper, further decreasing Wonkru's numbers.
In "Sic Semper Tyrannis", Octavia learns that Bellamy, Indra and Gaia have betrayed her, and so she makes them enemies of Wonkru as a whole. As of this episode, there are about 770 members of Wonkru.
As of "Damocles (Part 1)", approximately 300 members of Wonkru were left alive after the initial failed attempt to invade Shallow Valley. Some of them, who were branded as traitors of Wonkru, later rejoined the clan, with Madi as their new Commander.
After Kara Cooper's rebellion was prevented, Octavia took full control of Wonkru and became Blodreina ("Red Queen" in Trigedasleng). The title Blodreina is derived from a moment when Gaia became willing to accept Octavia as her leader and showed Octavia her bloodied figure in a mirror, stating that the blood of Wonkru's enemies was Octavia's armor, and thus an extension of her.
After Kara Cooper staged an unsuccessful coup with some other former Skaikru members to take the food supply for themselves, Kara, her fellow Skaikru accomplices, and other Grounder criminals were consequently punished for their decisions. This punishment, handed down by their new leader, Octavia Blake, was that of a gladiatorial fight for freedom, where only one indvidual emerged as the champion by being the last person standing. This event triggered the initiation of an institutionalized punishment system inspired by Bellamy's book about Ancient Rome, which he read to his sister Octavia as a child.