Timeline of Locke's Investigation

Immediately after the Beeson Job, Locke was held in a detainment facility pending investigation of his involvement in the loss of his agent. This means that the search for Ruan was conducted by the Hands and the upper levels of the Academy's leadership.

Once Locke was cleared of any collaboration or wrong-doing, he was returned to the Academy on Londinium. With this second (successful) escape attempt by an Agent, Locke arrived to find that changes were already being made. Attempts to further alter the programming of the agents as well as changes to the operator program resulted in the breakdown and subsequent culling of many of the teams he'd worked with for years.

During this time Locke himself was downgraded, going from an operator working the most secret of black ops missions to a sort of auxiliary private investigator. Mostly Locke was used to accompany negotiations with businesses owned by Blue Sun subsidiaries. He attended these meetings with his own security; ostensibly to protect him, but as a psychic, Locke was well aware they were there to keep him from running. When he wasn't working, Locke was kept deep within the higher security Agent level that he had once called “The Kennel”. He spent the long days between jobs waiting for the day that he would be culled like the others.

So, when Locke realized that his agent was still alive on Gonghe, he attempted to reestablish his tether which Ruan rejected (a combination of being out of practice and not understanding what was happening to him). Ruan then ran away and Locke slipped his own guard to chase him. Locke was quickly recaptured, but the Academy didn’t take the incident lightly.

Locke’s actions on Gonghe meant that security around him was tightened. Because it was so unlikely that their lost agent would be found within a casino on Gonghe, there were no attempts to investigate whether or not Ruan was actually there. Instead the focus was on Locke, whom they believed to be suffering a similar sort of mental breakdown to that seen in other operators whose agents had died. In these cases, the operators often believed that their agents were still alive and could still communicate with them psychically. Locke was examined and tested and deemed fit for work.

A short while later, when Locke again insisted that his agent was alive and on Persephone, it seemed very likely that Locke had broken down entirely and was no longer useful, even in his current limited capacity. He was returned to the Academy and this time, stayed there. Locke was lucky because though there were no more plans to further the tethered operation program, Locke and his agent had been one of the better examples of how well the system worked. There were plans to use Locke as an experimental model for future single agent designs and so he wasn’t immediately culled.

{I think somewhere around this time, River is stolen from the Academy by Simon.}

Locke didn’t know any of this though, and given the current political climate within the Academy, Locke didn’t have very high hopes for his future. What he did have though, was time and access to the Cortex.

Both on Gonghe and Persephone, Locke had not only intuited Ruan’s presence nearby, he had attempted to connect and felt Ruan actively resist him (though both times it felt strange, more like Ruan had panicked because he didn’t know what was happening rather than simply preventing Locke from establishing a tether). Because of their matched programming, for Locke, being blocked by Ruan felt different than being blocked even by another agent (whose head would have contained similar programming, but keyed to a different operator). Locke had identified Ruan as positively as if he’d found fingerprints. And so, frustrated by the Academy’s lack of confidence in their own work, Locke became obsessed with looking for evidence that his agent was alive. He wanted to show his keepers how wrong they were. More importantly, Locked wanted to survive. He needed to find Ruan, bring him back, and then maybe things could go back to the way they were.