Episode 8 is extremely confusing. In doing a deeper dive with other viewers, the consensus apparently is that The Enclave had young Hank McLean in their grasps from the beginning of the show being controlled by the original version of the microchip. Allegedly even before Brenda Howard removed the vile of cold fusion from his neck and even before he met Cooper Howard in the offices of Vaultech.
There is absolutely no evidence, no clues in either season to support this premise and the result is that it turned a great season 2 into a confusing mess.