It should end where it began
I think it should end with Beverly or Wen trying to reboot Eureka because they figure out that Jack was the reason they couldn't gain control of it.
They reboot it and Jack and his daughter decide not to stop and drive past Eureka. Wen or Beverly think they're rid of Jack but he gets into an accident with Allison as she's coming back to Eureka.
So like the Matrix, the Architect couldn't get past what he saw as an imperfection in humans that kept showing up as an anomaly in the system. Maybe the anomaly is the love between Jack and Allison.