Chaos, the primordial void entity who offers Boons through special Chaos Gates in the Underworld, has a questline hidden beneath the main game’s surface: they are a contractor for the House of Hades, and their working relationship with Nyx — Zagreus’s grandmother and the House’s chamberlain — has a specific history.
Reaching high relationship levels with Chaos requires accepting and completing their Boons across multiple runs, but the payoff is not a weapon upgrade or a new ability. It is a conversation where Chaos describes their relationship with creation and with the specific people in the House with a precision and intimacy that contradicts their presentation as an abstract primordial entity.
The secondary hidden content: the House Contractor offers upgrades throughout the game, paid in Gemstones collected during runs. Several late-game upgrades reveal that the Contractor is not a neutral entity — their work history in the House predates the current staff, and their dialogue after the True Ending makes references that suggest awareness of outcomes across timelines.
Supergiant hid relationship arcs inside background characters — the Contractor, the fish merchant, the Wretched Broker — that equal or exceed the depth of the main cast’s development. Players who engaged with every vendor as a character found a richer game than players who treated them as menus.

The attention to detail the developers put into this is insane. Most players will never see it but it makes the world feel so much richer.
This is the kind of discovery that keeps communities alive for years. Well documented.