When the Tenno stumble upon an Oculyst that is searching for Old War wreckage, the Lotus initially mistakes it for a Corpus drone. After further analysis and discovering that it is of Sentient origin, the Lotus abruptly cuts contact with the Tenno. Teshin agrees to assist the Tenno in learning of the drone's origins, which trace back to a tomb on Uranus that Tyl Regor is attempting to excavate. The Lotus suddenly returns, stating she was covering her tracks, but Teshin's endangerment of the Tenno and Tyl Regor's excavation have forced her exposure.
The tomb is revealed to contain the Sentient Hunhow, destroyer of worlds, who calls for Natah. While the Tenno reseal the tomb, the Lotus reveals that "Natah" is her former name during her time as a Sentient, and was in some way responsible for the fall of the Orokin Empire. With the Empire in ruins and the Old War over, she refused to complete the final sequence of her mission: destroy the Tenno. She instead chose to become their "mother" after she had become sterile during the Void crossing to the Origin system, hiding the Tenno in the "second dream" to preserve them and betraying her father Hunhow.
The Operator meets the Lotus on Lua, but before they can speak, Ballas suddenly appears and promises not to abandon "Margulis" again. The Lotus removes her helmet and holds his hand without question, and the pair vanish before the Operator. The Operator, now confused and alone, collects Lotus' helmet. With her absence, Ordis synthesizes her mission directives until they can figure out her whereabouts.
The Operator searches for the now missing Lotus. They hear a voice in their Orbiter's personal quarters, which shows them a vision of being confronted by Ballas, a pack of Sentient Mimic who are subsequently destroyed by Umbra, and an unusual and unique type of Sentient who kills Umbra.
It is later revealed that the unusual Sentient who vaporizes Umbra is none other than the Lotus herself, now in her true Sentient form, descending from the sky to rescue Ballas after he was fatally wounded by the Operator and Umbra. Shocked and confused, the Operator asks the Lotus what Ballas did to her, but the Lotus replies saying that Ballas did nothing as this is what she is before blasting off into the sky leaving behind a confused and troubled Operator.
Following The Man in The Wall to Lua and falling into the same chamber where the Operator encountered the Lotus and Ballas in the Apostasy Prologue, the Operator enters a portal where they discover Ballas, now Sentient-turned, cursing the Lotus for her deception, by stealing his perfect death. As the Operator overhears his rambling, his eye suddenly glows, which he implies it to be the Lotus' vision. He eventually relinquishes his sword , which he calls the "Sentient slayer", to the Tenno in preparation for war with the Sentients. As the Tenno grabs the sword, Ballas abruptly turns to face them and the Lotus' whisper calling for the Tenno can be heard.
The Jovian Concord
- Main article: Fragments/Partnership
Natah formed an unlikely partnership with Alad V, instructing him to create the Amalgams, Grineer/Corpus hybridized with Sentient powers. These new units, along with their combat data against the Tenno, would further serve the Sentients in their preparation for The New War.
During the mission to kill the Ropalolyst, Natah informs the Tenno them that the belief that she spared them as an act of mercy was false: rather that she was forced into doing so by the Orokin, and that they were both "imprisoned in Lua's belly", shedding light on the events of the Apostasy Prologue as a result. Natah also addresses that she "has seen the wall's other face", implying that during her time in her chambers on Lua, that the Void affected her as well with The Man in The Wall. Furthermore, she establishes the Tenno as the evil entity for the "destruction of my people" following the Ropalolyst's defeat, and foreshadows the events to come in The New War.
A flashback of the Old War shows Natah's original defection against the Sentients, and introduces for the first time Natah's own brother: Erra. He is shown attacking a wounded female Dax soldier in a huge cave full of Reservoirs under the surface of Lua, when Natah herself, already turned into the Lotus, intervenes with a group of Tenno (among which there is the Operator) ordering him to stop. Erra shows anger and sadness seeing how the "Makers" have made Natah, the "Queen of the Aphids", turn against her own family, blaming them for what happened, and then urges her to choose between her true family and the parasites, the Tenno. She, however, states that she is not Natah but the Lotus, and then proceeds to make the Tenno attack Erra with their Void Beams.
The Operator is then brought back in the present, finding themselves aboard a Sentient Mothership. In a situation similar to Chimera Prologue, the Operator assists to a dialogue between Natah, now returned to her original Sentient form, and Erra himself, who has apparently taken the lead of the Sentient army and keeps the Sentient-turned Ballas on a leash. It is shown how Natah is suffering from memory lapses, still believing the Orokin to be alive and to be during the Old War. Erra makes Ballas confirm that the Orokin are indeed dead, the "bios" (presumably Grineer/Corpus) are divided and only the Tenno remain a threat. Natah identifies the Tenno as the enemy and blames Ballas for creating them in order to face the Sentients. Erra however, points out how Natah now has "something our people never had before" and to be "stained by their wickedness". Natah reveals to be aware that the Operator is listening to their conversation, but both Sentients show not to be concerned by it. Erra then asks Natah to "sing" for all Sentients, calling them home and Natah proceeds to do so, knocking the Operator away and calling reinforcements for the upcoming New War.
Erra is telling Natah that their mother is gone and urges her to finish the war as she still has her fire. Natah notes that she remembers ordering the Tenno to attack Erra and he was apparently destroyed. Erra objects and states that she remembers wrong and will need time to completely heal from what the Makers had done to her. Natah points at leashed Ballas and asks if he is one of the Makers.
Erra then suddenly grabs and throws Natah at the pedestal behind him. She is trapped in some kind of trance and her body slightly expands. Erra tells her once more to finish the war and drops the leash from his hand. Revealing that Ballas's imprisonment was a deception, he stands as he and Erra silently stare at Natah.
Operation: Orphix Venom
- Main article: Operation: Orphix Venom
Following the Sentient's defeat at Operation: Scarlet Spear, Natah leads the second wave by teaching the machine-disabling Orphix to disable Warframes. The Tenno counter by deploying Necramechs, who are immune to the Orphix's pulse fields. As the war continues, Natah reveals to the Tenno her role in the Orphixes, but secretly transmits a code to them that says "I AM DYING".
Ballas tortures Natah/Lotus, turning her into a brittle husk while forcing her to watch Teshin succumb to a Narmer Veil. After presenting her weakened state to the Operator, Ballas steals her powers and opens a Void portal that drags her in. The Operator grabs her hand but Ballas slices off her arm with before stabbing the Operator, banishing them both.
The Origin System falls to Ballas's Narmer Empire. The Drifter, having somehow arrived in the Origin System and recovered the Lotus, now a dying Eidolon, teams up with Hunhow who desires not to see his daughter being used as a puppet. They steal Archon shards and deliver them to the Lotus, restoring her and eventually returning the Operator to the Origin System. After a long battle, they finally subdue Ballas and the Lotus steals back her power from him and ends his threat once and for all.
In the aftermath, the Lotus is conflicted with her personalities meshing between herself, Natah, and Margulis. The player can choose for her to revert to Natah, a Sentient that acts with decisiveness and strength.
- Palladino refers to the Lotus as Great Sentient Queen during Chains of Harrow.
- Erra, a Sentient warlord and a brother of Natah, stated that his sister is a "god" and a "queen".