The seed Siblings were in a large bunker specifically meant for the four of them. The deputy has prove to be a very dangerous enemy trying to eliminate the plans for new Eden...but could be useful. The deputy was drugged by Jacobs judges and brought back to him. Jacob took the Deputy to the secret bunker, so the Seed Siblings can finally decide on what to do with this problematic deputy. The deputy's hands were chained and he wore a muzzle, they couldn't risk anything.