John was relieved when "Harold Finch" finally made contact. Although he had needed to bunk down in various uncomfortable places during his military service, he was getting rather tired of living on the streets.
While Reese's official CIA file claimed he was killed in Ordos, the truth was John was deep undercover.
Finch was an irreplaceable asset-the upper echelons of the US intelligence community breathed a collective sigh of relief when he survived the "accident".
However, Finch had gone a little crazy due to the trauma of the accident and the loss of his best (and only) friend. But his skills were still intact, even if he did suffer delusions of interacting with an omnipresent machine. It was hypothesized that this delusion was a manifestation of his need to feel in control to prevent a similar accident, or possibly a response to guilt that he was unable to save his friend.
Regardless, Finch needed a babysitter. Someone to protect him from further accidents and to keep his delusion under control.
His previous babysitter was no longer an option. Grace would have liked to continue, as she found Harold rather sweet, but his delusion had convinced him he could no longer be around her (perhaps he had in some way picked up on the deceit?)
A psych profile was worked up to determine the most acceptable characteristics of Finch's new manager, and someone seemed to think that John fit the bill perfectly.
John was thankful that catering to Finch's delusion merely involved him helping people, rather than sitting around in a tinfoil hat waiting for instructions from the mother ship.
As "irrelevant" but unrelated activities were uncovered during routine intelligence operations in the city, the information was passed along in the form of a number.
Working the numbers kept Finch in nearly constant contact with Reese and safely secluded in the library out of harms way.
In fact, John was finding his little "missions" fun. It was certainly more satisfying than most of his previous covert work.
But John was uneasy about what it would mean for his situation if Finch ever figured things out. Finch was unwilling to seek any sort of help as he didn't feel there was anything wrong. Attempts to get him to talk with a psychiatrist, Dr Turing, had been a dismal failure. It had only exacerbated his condition, making him more paranoid and withdrawn. But if Finch's mental state ever improved so that he finally viewed the world rationally, John feared their partnership would be over.