High Prophet of Mercy

There's also another big idea, regarding the Prophet of Mercy.

Mercy was always the odd one out of the triumvirate. Where Truth and Regret were ministers used to scheming and political intrigue, Mercy was an old ascetic monk. When Truth and Regret were panicked and horrified as Mendicant Bias awoke and began to shake the Dreadnought free of its moorings, Mercy seemed to only watch in religious awe. From then on, he has no notable claims to fame. Whereas Truth and Regret are shown squabbling and scheming, trying to outdo one another throughout the war, Mercy is ostensibly a non-factor. He really does seem to be an ineffectual old mystic who was there just to keep him quiet and to complete the triumvirate.

But what if he wasn't? What if he was, in fact, one of the main reasons why the Human-Covenant War lasted as long as it did?

Nobody suspected Mercy could really do anything, the least of all Truth or Regret -- but in reality, he was a lot more shrewd than the other two younger Hierarchs -- or anyone else -- gave him credit for. Once the initial shock of the Oracle's divine proclamation wore off, Mercy became convinced that preserving and eventually elevating the humans was their Lords' will. It does make sense: he's the most pious of the three Hierarchs all and used to be the chief retainer of the Oracle itself. And he heard the Oracle call the humans his makers and his masters. To go against the Oracle's words would be the worst possible blasphemy for him. And indeed, we never see him express any opinion on the other Hierarchs' plan.

He still went along with Truth and Regret's big lie, reasoning that he could do most damage from the inside, while undermining them behind the scenes at every opportunity. Armadas bound for the human war found themselves stalled, the most competent commanders reassigned to deal with internecine unrest. Every time some upstart ministry staffer thought he was being clever and suggested that the Covenant try to look for radio signals to triangulate Earth's location, Mercy found him or her a comfy posting in a remote reliquary. Soon after, such triangulation was declared techno-heresy under dubious premises.

Recall Mercy's last words? "And this time, none of you will be left behind." The Hierarchs' conceit for exterminating humanity was that humans were Forerunners who had been left behind when everyone else went on the Great Journey. So what if Mercy's actual goal all along was to correct that ancient mistake and bring the humans along on the Great Journey? There's also the fact Truth left Mercy to die. Sure, it could be for any number of reasons. But maybe Truth also knew something, and had been looking to get rid of Mercy for a while, a sufficient opportunity just hadn't presented itself until that infection form latched itself onto Mercy's throat.