Spoilers are ahead for Halo season 2's finale.
Summary
- Kwan's connection to the Mother raises questions about her role in the larger Halo lore.
- Although unlikely, the theory that the Mother may be a manifestation of the Gravemind suggests Kwan is being manipulated for a darker purpose.
- It's more likely that Kwan has been given geas (or genesong) by an ancient Forerunner, which adds a weight to her destiny.
For the duration of its eight-episode run, Onyx, a planet with secret Forerunner connections.
Eventually, Kwan comes face-to-face with the Mother — at least in her mind. The cryptic character even saves Kwan from being subsumed by the Flood. However, in many respects, the "blessed ones" who are capable of activating Forerunner devices, that have crucial roles in Halo's larger lore. All of this has prompted one Halo season 3 theory to suggest that there's a secret (and much darker) link between Kwan, the Mother, and an ancient Forerunner enemy.

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Halo Season 3 Could Reveal That Kwan Ha was Manipulated By The Gravemind
Kwan Led Miranda & Dr. Halsey To The Flood Sample
When Kwan lands on Onyx with Master Chief and the other creating the Spartan-II program. Halsey attempts to lead the way, but Kwan actually guides the unlikely pair through the installation, thanks in large part to the Mother. Kwan and Halsey meet up with Commander Miranda Keyes (Olive Gray), who's attempting to continue Halsey's long-abandoned research.

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Years ago, Forerunner scientist clutching a device, which contains Flood spores. Without Kwan and her visions, Miranda would never have found the Flood, suggesting Kwan may have been manipulated by the Mother into indirectly unleashing the Flood.
At first, the Flood is feral, infecting and hijacking any sentient lifeform in its path.
If The Mother Is A Manifestation Of The Gravemind, It Explains How She Stops The Flood
The Mother Is More Likely A Forerunner
The theory suggests that if the Mother is actually an agent of the Flood, she could be a manifestation of the Gravemind. Referred to as the Ancient One in Halo's core canon, the Gravemind is a compound intelligence — that is, the shared consciousness of the entire Flood species. In the games and books, the Flood undergo various stages. At first, the Flood is feral, infecting and hijacking any sentient lifeform in its path. Once it overtakes an entire ecosystem, however, it enters the "Coordinated Stage," allowing the Flood to generate a hive, propagate spores, and unleash a Gravemind.

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A compound mind that inhabits all Flood forms, the Gravemind emerges once all available lifeforms have been infected by the Flood. Although it manifests as a tentacled, worm-like monster in the core canon, the Silver Timeline might take a different approach. During the Coordinated Stage, the Flood is more organized and able to communicate telepathically. Interestingly, once the Flood infestation consumes the entirety of the Onyx base, the Mother is able to communicate more clearly with Kwan. While the Mother being a Gravemind form explains how she saves Kwan from the Flood, she's more likely connected to the Forerunners.
"I knew you'd find me," the Mother says when she s Kwan telepathically.
The Halo Season 2 Finale Hints More At Kwan’s Genesong Than A Gravemind Twist
Kwan’s Geas Connects Her To The Forerunners
The Mother's uncanny ability to freeze the Flood-infected humans in their tracks is incredibly jarring. If she is the Silver Timeline's spin on the Gravemind, her ability to manipulate the hive mind makes sense. "I knew you'd find me," the Mother says when she s Kwan telepathically. "We knew you would deliver us." While those lines strongly hint at a twist — that Kwan was being manipulated by a Flood agent — the Mother's other lines suggest otherwise. "I am you," the Mother says, before calling Kwan a "Protector" and telling her that all of her ancestors are "within."

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One of the biggest questions that's plagued Halo season 2 since episode 1, "Sanctuary," hinges on the identity of the Mother and her link to Kwan Ha.
The Halo season 2 finale doesn't delve into the history and origins of the Flood, but it makes the threat it poses abduntantly clear. The Mother tells Kwan that the Flood desire submission, to cohere everything to them. In the core canon, geas (or genesong) is a Forerunner term that describes a "genetic command imposed on an organism or species" (via Halopedia). A lifeform under the influence of geas follows a set of subconscious orders. Sometimes, those orders are ed on, lasting many generations, which feels more in line with Kwan and The Mother's connection than a Gravemind-type twist.
How Kwan’s Destiny Intersects With Master Chief’s Role
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After Dr. Halsey discovered the Forerunner and human DNA on Onyx, she searched the galaxy to find candidates with a very specific set of genetics to become her Spartan-II soldiers. This notion teases that Master Chief (and maybe his fellow Spartans) are Halo's Reclaimers. In the core canon, the term "Reclaimer" is used by Forerunner constructs to refer to humanity — the species that received the Forerunners' Mantle of Responsibility and became custodians of all life in the galaxy. This explains why humans can use tech like the Halo Array, so the show's "blessed ones" echo the Reclaimer idea.
The term "Protector" also has origins in the core canon: they are Forerunner machines built for fighting the Flood.
It's hard to know if the Paramount+ series intends to use the "blessed one," "Reclaimer," and "Protector" interchangeably. Kwan's status as a Protector could mean something else entirely. Plus, while the Mantle of Responsibility and geas seem to share some commonalities, they are very different concepts. Only highly skilled Forerunners were capable of creating geas and imposing them on a lifeform, whereas the Mantle of Responsibility is more of a species-wide charge. Still, Kwan and Master Chief's destinies will probably intersect a lot in Halo season 3, especially as the Flood grows.
All 8 episodes of Halo season 2 are now streaming on Paramount+.
Source: Halopedia