Soooo... How did they put the barrier back up if the thingamajig that makes it happen was stolen?
Oh and yeah - drama incoming.
Isana tells the citizens that "the ruins are moving to protect the city". It sounds like the city's ancient defense systems were reactivated, namely the relic-mecha and the defensive barrier. So maybe the holy stone that was stolen is no longer necessary for the barrier.
It's unclear what awakened the ruins, but it's possible that Isana's desire to protect Hime was the key. The relic-mecha was able to find her in an instant, so she should have a special connection to the city. That same connection is likely related to the memories she saw of the city from a long time ago.