Ezio wrote:
Sera Works For an Espionage-Related Organization
In File 769, Sera suggests that she has sharp ears "due to her line of work" (pg 2), suggesting that she works for an organization that involves stealth and information gathering. She also suggests that she has witnessed "innumerable" jumper suicide scenes (pg 3), suggesting that the organization she works for also involves dealing with homicide cases.
You know who else has a job that involves stealth and information gathering? Bourbon does.

I'm not too sure, if you really run into all that many suicides as an FBI agent. A BO member, however, might find it necessary to stage these, and thus know how to do it correctly.
Sera Has Detailed Knowledge of the Japanese Police Force
In File 773, just by noticing a flickering light outside the Detective Agency windows, Sera recognizes the presence of the police, the number and name of their units, their tactical positions, and their plan to defeat the bomber in a very short amount of time. She also goes as far as to help them in their plan by luring the bomber to the window to allow the snipers to shoot him (much like how a normal police officer would act). The source of her knowledge and expertise is unknown.
The FBI doesn't really find it necessary to cooperate with the Japanese police force on this, so an extensive briefing on this would be unusual. The BO however has to know a lot about the them, since they are one of their enemies.
Sera is Highly Skilled in Martial Arts and Deductive Reasoning
Sera displayed her skill in martial arts in File 768 when she counter-attacked Ran (who is an exceptional martial artist herself). She displayed her deductive abilities in File 769 when she deduced that the jumper-suicide was actually a homicide disguised as a suicide.
Ran is highly skilled in martial arts, Shinichi in deductive reasoning, neither is an FBI agent. Bourbon is said to be a highly skilled in deductive reasoning.
Sera is a Japanese-American That Moved Back to Japan Recently
In File 771, Sera tells her classmates that she moved back to Japan after living in the United States with her parents for a period of 3 years (pg 2). Apparently, the reason for her return to Japan is that it is "easier to be a detective", suggesting that she is working on some sort of case.
She moved to Japan because the plot needs her.

Doesn't work as proof for anything.
Sera Has a Possible Connection to "Deceased" FBI Agent Akai Shuuichi
In File 771, when scolded for his actions in the previous case by Haibara, Conan says that Sera is "not an enemy" because she resembles someone he met before (pg 11). Conan has previously worked with Akai during the Clash of the Red and Black. Sera physically resembles Akai (compare the two faces, especially the eyes) who is also a Japanese-American. Also, as some people have mentioned, the name "Sera Masumi" is very similar to the name "Sayla Mass" (Seira Masu), who is Char Aznable's younger sister in the Gundam Wing anime franchise (Akai is named after Char Aznable himself). Also, Sera mentioned that she moved to America three years before the current timeline; this was around the same time when Akai infiltrated the Black Organization as "Morobashi Dai".
Yes she is, but that doesn't mean that Sera is also one of the good guys. Conan's just a twat.
Sera is Investigating Conan
Interestingly, Sera seems to know Conan's name as well as the fact that he is a "detective" despite it being their first time meeting each other. She also knew Ran as well as Professor Agasa (file 771). The source of this information is unclear, however, Haibara points out that Conan's name has come up in newspapers due to his battles with Kaito Kid. She also goes as far as to purposely get her deduction wrong in order to let Conan solve the case himself, probably to test his deductive abilities. In File 771, she shows extreme interest in meeting Conan face-to-face, and alludes to the fact that Conan is the "brain" behind Kogorou's deductions. In File 773, she hints to Ran about the connection between Conan and Shinichi, possibly meaning that she knows or suspects Conan's identity. The reason and motive behind her investigation are unclear, however, it is possible that she is investigating Conan because he had contact with Akai shortly before he "died".
And when she knows who he and Ai are, why investigate them clandestinely? And why is Subaru not thrilled to see her at all and starts to trail Ai after he sees her?
Putting the Pieces Together:
Sera works for an espionage-related organization and has exceptional skills in martial arts and deductive reasoning. Her skills in martial arts and deductive reasoning might have been obtained while she trained and worked for the organization. She is willing to have criminals killed (like she did with the bomber in file 773), probably due to the fact she witnessed countless deaths during her work in this organization.
Quite speculative. An utilitarian attitude also fits with being a BO member, as do her skill.
This organization is most likely the FBI, due to the fact that Sera lived in America recently (the FBI is an American organization) and has a possible connection to a "former" FBI agent (Akai).
The BO is also active in the US, and having a brother in the bureau doesn't mean you also become a member by default. Having a sister in the BO might have made infiltrating easier though.
She has detailed knowledge of the Japanese Police Force; she might have received this information from her fellow agents in Japan to prepare herself for her investigation.
Why? She's not investigating the police at all. And if she were an agent, then this is not an official task, or why isn't she with the others?
COUNTER-THEORIES:
"Sera is Too Young to be An FBI Agent" - Sera's True Age Has Not Been Revealed
Many of you have been arguing that Sera might be too young to be part of such a high-level organization. However, even though Sera showed up in Ran's class as a high school student, her true age (as well as her identity) has not been confirmed; assuming that she's an FBI agent, she could have forged the papers necessary to register for school, which would allow her to act as a high school student. I would also like to mention that Jodie Starling (a current FBI agent) is around 28-29 years old, and has been a member for at least 5 years (it was shown in flashbacks that she was a member during Akai's time in the Black Organization), making it possible for a young woman such as Sera to join as well.
"They're due to pop out any day now"
A woman in her early twenties wouldn't really hope for her breasts to grow anymore, meaning she is probably really 17ish.
"Sera is a Black Organization Member" - Not Likely
Some of you have mentioned that Sera could also be a member of the Black Organization. This theory is not very likely, due to the fact that Sera publicly worked with the police to solve a case (Files 768-770).
Scar Akai has also helped towards solving a case in the past albeit less directly.
If Sera was called in for questioning by the police, her identity as well as her involvement in the organization would have been exposed. If she was a BO agent, she would have a certain cover/identity; this identity can easily be exposed if she was questioned and interrogated by the police (for example, if she was a BO agent and an undercover high school student, the police can expose her identity by revealing her true age). This is out of character for the organization, as they would avoid contact with law enforcement during their work (similar to how Gin and Vodka acted in the first chapter of the series).
Yeah, because the BO definitely doesn't have the skills to forge documents that look the least bit legit.
Gin and Vodka had incriminating documents on them in chapter 1. She also doesn't have a fake ID with her supposed age, because where the hell would she get that from?
"What if Sera's identity as an FBI agent was exposed?" - Easily Excusable
If Sera is an FBI agent and came to Japan to work on a mission, her identity could be exposed. However, this is not an issue because Sera can make an excuse for her stay in Japan such as visiting a relative, vacation from work, or going back to high school to finish her education. Jodie and Camel did the same thing when they were uncovered by Takagi and Megure during the Clash of the Red and Black (File 606).
I hope you enjoy my theory, and please feel free to leave comments and/or counter-theories to prove me wrong.
That's mainly proof that the police don't like to dig and wouldn't uncover a BO-faked identity either.