Scar Akai is Bourbon theory

Scar Akai is not the real Akai

Scar Akai is right handed, not left handed like Akai

Scar Akai used his right hand to fire a handgun and to hand back a cellphone. It is unlikely scar Akai is simply using his right hand because he injured his left. In the "Teito Bank Heist", he easily escaped the duct tape binding his hands, yet probably did not use the same method that Jodie used because there was still duct tape over his mouth. It doesn't make much sense for him to put the duct tape back over his mouth again afterwards. Removing the tape with only one hand, especially if it's his off hand, would be difficult especially if robbers are watching him. (His eyes were covered so scar Akai couldn't be sure that no one was watching until the robbers pretended to be hostages which would give him only a few minutes to escape.) Switching handedness after head trauma does not appear to have been documented in scientific literature.

Scar Akai's behavior does not make sense if he is Akai

If scar Akai is the real Akai, one must assume he either has his memory or he doesn't have it.
If he has his memory, Akai would absolutely not wander around in the open since it puts Hidemi (Kir) at risk with no gains to be made from doing so. The Organization's actions in the "Thirteen Red Shirts" case demonstrate the danger.

If Akai does not have his memory, then it is plausible Akai would walk around in the open without knowing the danger he is in, however Akai's actions strongly suggest his memory is still intact. He seems to be stalking the FBI by appearing before them: something he would not do if he had lost all of his memory. Further emphasizing the point, Akai also apparently left a warning message to Jodie on her drink coaster during the events of the thirteen red shirts case. If perhaps scar Akai recognized the FBI a little and felt comfortable enough to leave Jodie a message, it is strange that he would not speak to the FBI agents since Scar Akai is clearly capable of speaking. Scar Akai also appears to recognize Chianti.

A more reasonable explanation is that Scar Akai is not Akai and avoided speaking because he is unable to imitate Akai's voice. The person in disguise as Akai is trying to gauge from the FBI's reactions whether the real Akai is dead or not.

Gin's actions suggest that he doesn't think Scar Akai is the real Akai

Since Gin called Kir in the "Thirteen Red Shirts" case, he has held a gun to her head the entire time. After Gin observes scar Akai, he gives the order for Chianti to leave, and he lowers the gun from Kir's head. While Gin might not have wanted to shoot someone with an unsilenced gun in front of a busy department store that is filled with police, if he thought that Kir was a traitor who had helped Akai fake his death, Gin would not have lowered his gun since Kir may attempt to retaliate in some fashion now that her cover has been blown. The lowering of the gun is concession on Gin's part that he knows or strongly suspects scar Akai isn't the real Akai.

Scar Akai is probably a Black Organization Operative rather than an FBI agent, a CIA agent, or a third party

Scar Akai almost certainly isn't in the FBI or CIA because his wandering about in the open disguised as Akai is threatening Hidemi who is an asset to both alphabet agencies. There isn’t a single beneficial reason for an FBI or CIA agent to appear in public as Akai, and everything to lose by doing so. The obvious remaining choices are that scar Akai is a member of the Black Organization or a third party. If scar Akai is a member of a third party, then perhaps he is trying to lure the B.O out with a disguise because he knows Akai was serious threat to them and apparently died; however, this means the hypothetical third party scar Akai doesn't care about or doesn't know about Hondou Hidemi being a spy. If a third party was interested in luring out the Org., then simply appearing as Akai somewhere would be enough. Specifically appearing with FBI agents puts the agents at risk. Since most third party intelligence or police organizations like Interpol or the PSIA (Japanese intelligence agency) would be allied with the FBI or the CIA, they would avoid doing this. Another issue is that the existence of Interpol or PSIA agents investigating the Org has not been hinted as was the case with the FBI in the Vermouth arc or CIA in the Kir arc. It is possible that scar Akai may be a member of a rival criminal organization, but again there is no evidence of one existing. Finally, third parties run into the problem of how exactly they found out about the circumstances of Akai’s death well enough to time their agent’s arrival and appearance to match Akai. In conclusion the most likely option is Scar Akai is a member of the BO.

If scar Akai is a Black Organization operative, then he is most likely Bourbon.

Most importantly, at the Beika dept. store case, Scar Akai showed up at the same time as all the other known codenamed B.O. members except Bourbon (and the boss). The conversation with Gin, Vodka, and Kir about Bourbon (703.03) does imply that Bourbon is a real person rather than a made up agent meant to test if Kir was leaking information. Gin’s comments about scar Akai suggest Scar Akai is Bourbon. If Gin isn’t talking abut Okiya who is Akai (who Gin doesn't know about) then that leaves scar Akai as the subject of Gin’s monologue. (704.13) (704.14) Gin: “Hmph... Always doing as he pleases... that bastard irritates me.” Kir: “Eh? Who?” Gin: “……… Just as you said…Someone you wish was only in a novel… A great detective, like Sherlock Holmes…” Gin's line about scar Akai “always doing as he pleases...” implies that Bourbon is doing things on his own, which Gin said Bourbon tends to do. (703.03)

Scar Akai's actions –even the seemingly contradictory ones- can fit with what we know about Bourbon's motives and personality

Why would Bourbon be in disguise as Akai? - Bourbon is trying to evaluate whether Akai is dead or not.

Bourbon's motive - He doesn't believe Akai is dead

Gin and Vodka saw Akai’s “assassination” carried out, so this would appear to negate any reason the Org would have to look into Akai’s death; however, Gin spoke to the fact that Bourbon hates Akai with a passion and believes he is the only one capable of killing Akai Shuuichi and is therefore likely to suspect a trick in the FBI agent’s death. (703.03) Thus, Bourbon probably has a desire to investigate Akai’s death.

Bourbon's mission - Disguise as Akai to test the FBI's reactions.

So far, scar Akai has only been appeared in front of FBI agents rather than around Tokyo generally. The obvious reason for a Black Org member to do so would be to gauge from the FBI's reactions to the disguise whether Akai is really dead. The FBI agents scar Akai has appeared in front of so far, Jodie and Camel, were known to be close to Akai and thus would be considered likely compatriots if Akai needed help faking his death.

Bourbon's disguise- Created with help from Vermouth

The conversation between Gin and Vermouth about getting the boss's approval (V67-8 pg 11) can be interpreted as Vermouth informing Gin of Bourbon's plan to disguise as Akai with Vermouth's help and test the reactions of the FBI agents. In that scene, there is a panel with no speech where Vermouth faces Gin. It seems pointless at first, but it makes sense if it signifies conversation between Gin and Vermouth that the readers were not allowed to hear. At this time, Vermouth informs Gin that scar Akai is Bourbon in disguise, and she that helped with that disguise as part of a plan to test the FBI's reactions to him to see if Akai is still alive. Gin asks if Vermouth got authorization from the boss to go through with this plan and disguise Bourbon as Akai. Vermouth affirms this and explains that the boss is cautious and wants to make doubly certain the FBI didn't plan a trick with Kir to fake Akai's death. This conversation implies that the Org lied to Kir about Bourbon's true mission so that Kir couldn't alert any FBI colleagues that they were going to be probed. Kir was told Bourbon was looking for Sherry. (703.03) Vermouth's help with the disguise explains the discrepancy between the excellence of the scar Akai mask, but Bourbon's inability to mimic voices which requires him to pretend he is mute. Bourbon damaging his mask by removing the tape covering his eyes in the Teito Bank heist explains the artistic reasons upper part of scar Akai's face was drawn in shadow and the gun was positioned to hide the damaged scar. (V65-5.14)

Bourbon's investigation- He suspects Kir is a traitor.

As additional evidence, scar Akai has Kogoro’s cellphone number either memorized or specifically noted down. I doubt Kogoro has a webpage with his cell number on it, and the landline still seems to be the primary call route for first time clients as of the Kir arc. An obvious explanation for why a Syndicate operative would have Kogoro’s cell number is that scar Akai got it from Kir’s phone which has a text message from Kogoro that was sent sometime after the Ding-Dong-Dash case (499.16). It would be impossible for Akai to fake his death without Kir being an accomplice so Kir would be a natural target for anyone investigating. Kogoro would have sent the text message later since I assume he had to look up the routing number because he didn’t give her the number immediately at her apartment. Her cellphone was probably left in Gin’s car after she changed clothes following the failed first round of Domon’s assassination (502.15), and she would have probably used a radio with a mike like Vermouth because she was on a motorcycle and wearing a helmet. (503.9) As long as no one else fiddled with her cellphone while she was in the hospital, it is unlikely the message was erased before Bourbon would have the chance to get to it. Bourbon may have reason to investigate Kir even before Akai “died”. He may have been suspicious of how easily Kir was recovered, and he suspected she is a spy who planned something with Akai.

Why would Bourbon protect Conan in the Teito Bank Heist case? – There are several possible motives

By far the most difficult and mysterious action to explain, I doubt the reasoning behind Bourbon’s rescue will be resolved satisfactorily until we get more information on how much Bourbon knows about Conan and more details about Bourbon’s personality. At the time of the shooting, Bourbon may or may not have recognized Conan Edogawa is Kogoro’s live-in brat who was present during the Ding Dong Dash case and (if he knows) other FBI related cases as well. Potential motives can fall into two groups: motives that don’t require Bourbon knowing the boy is Conan Edogawa; and motives that are based on Bourbon recognizing Conan .

Potential motive that doesn’t require Bourbon to recognize Conan.

If Bourbon is wearing a mask, it is likely his disguise was messed up when he removed the duct tape. The anime shows the scar and presumably the rest of the mask intact, but the manga doesn’t make it clear in either the gunshot scene (679.14) or the video scene (700.02) whether scar Akai’s mask is intact or not. The anime may have made a mistake. Bourbon would want to leave the bank quickly while Jodie is unconscious so she doesn’t see what he really looks like and realizes the truth. Firing a gun would bring the police rushing in and would stir up the crowd providing cover. It would also mean Bourbon could leave that much sooner.
It is true Bourbon could have fired the gun at the ceiling or similar, but I suppose firing a gun at someone’s attacker would be less suspicious than firing at the ceiling in the eyes of the investigating police. Also Bourbon may have found Conan interesting: Conan did botch the thieves plan and use the voice changer after all. Lastly, if Bourbon wants to convince Jodie he is Shuu, then rescuing Conan would make the most sense since that is what Akai would do.

Potential motive that does require Bourbon to recognize Conan.

The details of this motive will depend on how much Bourbon knows about Conan. If Bourbon has access to any Black Org. intelligence as would be expected of someone specializing in intelligence gathering, he may have realized that Conan or at least a kid of matching description has appeared at several FBI or Black Org scenes. The more Bourbon knows about Conan’s connection to the FBI, the stronger Bourbon’s motive for wanting to make sure Conan is around to watch or investigate since Bourbon may not get all the answers from his other lines of investigation.
At the very least, Bourbon would recognize Conan from the Ding-Dong-Dash case since Bourbon already has info on Kogoro from that time because he knows the detective’s cellphone number offhand. Beyond that, Bourbon may also recognize Conan from the case and news-story about Akemi’s death. Bourbon would most likely have taken note of that since Akemi was close to Akai. The next level up in importance (and danger to Conan), Bourbon may also know about times where Conan interacted directly with the FBI like he did at Haido Central Hospital during the Red vs. Black arc. Akai did warn Conan that his face would be known to the Org then (597.08), and Vodka did say another man was sent in after Kusuda Rikumichi disappeared. (599.02) (Perhaps it was Bourbon, but I doubt he would be under Vodka's orders.)
Because of Conan’s connection to these cases, Bourbon may intend to question or observe Conan later if none of his other information fishing methods pan out. I assume Bourbon doesn’t have too deeply incriminating info on Conan because if Bourbon realized how brilliant Conan was and knew that Conan and Akai had a working relationship and spent time planning together, then Bourbon would have chose to investigate Conan before Jodie or Camel.

Why would Bourbon not tell the other B.O. agents what he is doing? – Bourbon has a secretive personality.

I doubt Bourbon would expect much help from his fellow operatives seeing as how Gin, Vodka, Vermouth, and Chianti assumed that Akai was dead. Also, Gin specifically pointed out that Bourbon was, “like Vermouth, he’s [Bourbon] a secretive one… I have no idea where he is or what it is he’s doing...” (703.03) Bourbon is a lone-wolf secretive agent and hasn't kept Gin and friends in the loop about his private investigation on Akai’s death.

Why would Bourbon do something risky like text-message Kogoro? – Bourbon isn’t adverse to taking risks.

Bourbon has consistently engaged in behavior that can be seen as risky: he chose to appear in front of the FBI dressed as Akai despite not knowing how they would react, he shot the robber holding Conan in the bank, and he didn’t tell his fellow operatives about his disguise-as-Akai plan which almost caused him to be shot by his own side. Bourbon was cautious about mailing Kogoro in that he made sure to leave no fingerprints on the random man’s phone he “borrowed”.

How could Bourbon tolerate disguising as his most hated enemy? – Bourbon is willing to suck it up because he wants to find out about the condition of the real Akai.

Besides evaluating the FBI agents’ reactions to seeing “Akai,” scar Akai may potentially be attempting to infiltrate the FBI. I don't think scar Akai is attempting to infiltrate the FBI but I thought I would throw that possibility out there. Also, appearing as Akai will rub salt in the wounds of the agents who cared about him. Bourbon might be vindictive like that.