A/N: This story takes place about a day after the final chapter in my Chuck vs the Doctor story. I suggest you read it in its entirety before reading this story to get a better understanding of what is happening. I have provided a brief refresher summary covering most, but not all of the previous events of the preceding story.
Prologue
Previously in Chuck vs The Doctor:
Embarking on a small surveillance mission turned into a starting point for Sarah and Chuck's real relationship. Shortly after the mission, Laslo obtained and contacted Sarah on her cell, providing her with important details regarding the intersect and the potential deadly hazards they could face from it. Through a series of events during the mission and at their after mission 'party', they had come to an understanding on their relationship. Casey had been monitoring the two and informed them he would keep the information from HQ as long as they did they jobs effectively. Unfortunately as is common in the Chuck universe, not everything goes to plan and shortly after their 'party', Chuck and the team was captured by an unknown entity for unknown reasons.
Initially Sarah and Casey were kept in a room separate from Chuck. When Chuck realized the rest of the team were in an adjacent room he worked to reunite them. It quickly became apparent that they were being forced to function as lab rats in an elaborate psychological experiment, with Chuck as the hinge point. The 'Doctor' was the lead man in charge and all instructions were relayed and carried out through his personal assistant, Mary.
As part of the mental assessment, Sarah and Casey were eventually released with Chuck's help, but only at the whim of the Doctor. The agents were unaware of who had helped them escape and had been tricked into believing that Chuck was safe at home. Later the Doctor manipulated the agents into thinking he was torturing Chuck to death for helping them escape. In light of their new commitment to a real relationship the potential loss of Chuck hit Sarah quite hard and she was showing signs of emotional instability affecting her performance as an agent.
The Doctor monitored their return into the facility and a minor problem with some of the Doctor's staff created a dilemma for Sarah as she briefly snapped and brutally killed a man. She recovered somewhat but with a gap in her memory of violence moments before. The mental instability was added to the psych records the Doctor was keeping. Sarah did seem to regain her full faculties after successfully reaching and saving Chuck, suggesting an extremely deep emotional attachment to Chuck.
Meanwhile Chuck had gone through his own series of trials and tribulations; discovering some new found abilities, while dealing with the experimental drugs the Doctor injected into him, and meeting the sexy but strange assistant.
During the course of Team Chuck's incarceration, it became apparent to the readers that the Doctor was on a contract mission for a firm or agency known only as the 'Office'. Mary, his loyal assistant, also found out he had one or more side contracts with some high profile clients, overlapping on the current mission.
The eventual escape of all Team members was allowed to happen at the whim of the Doctor and was achieved through a combination of Chuck's new abilities and minor help from Mary. Mary also forwarded a warning and a video msg of Sarah insanely killing the man earlier, to Chuck's phone. While he did see the video, he received the warning too late and the escape was marred as Sarah was critically injured. Chuck's insane race to the hospital to save Sarah allowed Casey to see some of Chuck's new abilities in action, leading him to draw serious conclusions about Chuck's background as a potential deep cover agent, working against them. Casey just needed proof. It also provided Casey with direct evidence that Chuck was as emotionally attached to her as she was to him.
The hospital stay was relatively uneventful after Sarah was admitted, and when out of surgery Sarah and Chuck shared a short but welcome moment together with hints of more to come. After being kicked out of her room Chuck took a break and met up with Casey for some grub. During the meal he succumbed to the lingering effects of the Doctor's experimental compound. Unbeknown to Chuck, one of the major points studied by the Doctor was how relationships and intimacy triggered biochemical reactions that inhibited the pain inducing compound. For Chuck his concern for Sarah and their fast growing relationship was minimizing the pain compound the Doctor had given him. Now that she was safe, his natural resistances had dropped, and he was feeling the full effect of the drug.
All test data was forwarded electronically to the Office, but not before Mary altered some of the information. Following Office procedures all data at the facility location was destroyed. Shortly after the destruction of the facility, the Doctor listed the new compound on a secure Office site, with previous customers including the CIA, NSA and other notable government organizations. After finding out that the Doctor had been skimming her profits from missions and was officially retiring, she decided a change in her life direction was due. The Doctor, unaware of her revelation, invited her to come live with him, as he was retiring. Mary made a plan to 'collect' the money owed and get some revenge.
Casey made a late night stop at Sarah's room before reporting to HQ. The visit quickly turned into a relationship counseling session for Sarah ending with Casey bluntly telling her that she is just as screwed up as Chuck and they both needed some sex to relieve months of tension. He left no further ahead than when he entered.
Mary also had plans for Chuck; having left the Doctor under the guise of running some last minute errands before she came to live with him . She would visit Chuck to take sperm samples, knowing that the drugs she would use and the method of collection would trigger his innate resistance for long enough to see the compound dissipate from his system.
Sometime later Sarah woke, and after a short stint of news watching and a conversation with Casey, she was informed of Chuck's coma like state and taken to see him. During her visit Mary was able to bypass security and remove both agents from Chuck's room for long enough to extract the samples.
Returning from the bogus tests, Sarah unknowingly met Mary on her way out of Chuck's room. Moments later Casey walked into Chuck's room, only to surprise Sarah in an embarrassing position. He had been there to inform her that Ellie had arrived at the hospital looking for Chuck. As Casey had not remembered to phone Ellie, she eventually showed up in a very unfavorable mood, having somehow figured out where Chuck was.
The ensuing interaction with Sarah was somewhat volatile, as she confronted her in private over Chuck's behavior, demanding under threats of bodily harm, what Sarah's intention with Chuck really was. Sarah, while twisting the truth about the recent events and hiding any government involvement, remained fairly factual on the information and eventually admitted to Ellie that she was in love with Chuck. The admission, coupled with some other information Sarah shared, led to an amicable understanding between them.
About the same time Sarah and Ellie bonded, elsewhere in the city Mary received news that the sperm samples she got from Chuck indicated he would be an excellent genetic match and father to their children. In the meantime she was finishing final preparations to kill the Doctor with a method that even the Office would not fault her on.
The events of the following story take place in the early afternoon hours of the following day.
