Well, let's see. Do you intend to continue with other adventures in series? That is a rather large turn, after all.
How I'd do it, to least screw up the rest of the plot-line, is have Indomitability endow its essence into one vessel, some person who is important to the Gate Pass resistance, to make sure that person doesn't die. Then, the trillith can grant his boon to various agents of the resistance whenever they go on missions, and can incrementally help cut down on casualties among the citizens.
If he's not bonded to the forest, he doesn't have the same scope of power, and unless you want to invent some item or location that is as key to the nature of Gate Pass as the sword of Anyariel was to Innenotdar, Indomitability won't be able to have the same bond with the city. He won't be able to keep the city from taking damage, or save everyone inside from dying -- at least not yet. For now he's a useful ally who can help ensure that the city is able to hold out against its aggressors.
Later, though, after he's had time to explore the nature of the city's unusual connection to dreams (i.e., when the party is higher level), he can reclaim the power he possessed in the fire forest. Of course, the Ragesians know about trillith, and would have the ability to destroy Indomitability once they figured out he was responsible for the odd resiliency of the Gate Pass resistance.
In my campaign when I ran it, the heroes kept Indomitability's boon, and the 'paladin' of the group convinced it to manifest and serve as his mount for particularly critical encounters. Not quite as impressive as having it make your city invincible, though.
Cool scenario.