By letting Lennon do what he wanted without any hindrance they made him believe that he was free, left unwatched.
He pranced along, making his little plans thinking that he is alone. Of course, Jake was smart to have himself included and made records of everything.
No one can save Lennon.
And Robert Milroy was sent by Gordon Faraday. Agnes wouldn't have approved of using Rory as bait to this extent but Rory got to that on her own.
When Robert Milroy told them that Rory wants to travel to LA secretly, they purposefully put her on the same flight Lennon was taking.
Lennon used that secret airstrip that was not listed in any database to make his secret travels to the town. That's how he made sure that there won't be any official records of him being in the town whenever Rory was stalked. And this was not the only secret airstrip Lennon used.
But everything has receipts. Lennon thought he is safe. Lennon thought that Rory was stupid.
