Shiho will be the likely motivator because Shiho's issues have completely taken over Akai's plot now that his past has been relatively sorted out; Akai "broke" his promise to Shiho to protect Akemi, he is waiting for the right time to talk to her, and I think it is likely Akemi asked Akai to look after Shiho in the PS of her last text message.
I believe a dramatic rescue is much more likely than a no-danger verbal showdown between them. Akai really hasn't had a strong hero moment specifically with Shiho yet. Ran jumping on Haibara overshadowed his forcing the Black Org back during the showdown with Vermouth. He protected her a few times as Okiya, but those moments were pretty weak, especially in the train case where he basically just scared her into hiding and nothing was really resolved.
TLDR: This Akai/Shiho business is happening because Gosho is probably setting up Akai to rescue Shiho
On a slightly different note, this sort of plot obligation logic is really useful for predicting how the story will go next. The lack of real resolution in the train case and remaining unanswered questions signal that it was not the climax, the Bourbon arc is still running, and more drama will eventually happen. While that seems pretty obvious, stating it outright like that makes it easier to pick apart the plot Gosho is trying to create. The train case identified the identities/allegiances of the various mystery characters, set Sherry's status to dead, made sure Akai's status remained unsettled for Bourbon, and centered Bourbon's attention on Conan's identity.
My predicted plot obligations are as follows assuming we will return to "standard Conan plot" eventually:
- Akai is going to save Shiho at some point as mentioned above. Shiho will also have some sort of confrontation with him to resolve Akemi. Akai knows Conan's identity and it will be relevant sometime.
- Shiho cannot stay out of danger forever; her BO plot role since her first appearance was to be hunted down and it will take the destruction of the Org by Conan to stop it. Also the confrontation with Akai needs to happen.
- Conan always has secret identity leaking issues. Ran has some slow building suspicion. Sera has been asking the same sorts of questions as Eisuke. Amuro is now looking into Conan. Akai knows it already but will eventually have to talk about it.
- Amuro is going to need to have a real face to face showdown with Akai. He can't not after having his hate and rivalry set up; he'd be completely impotent as a character otherwise. Also we have Date to resolve.
- Sera seems pretty well patterned after Eisuke[2], so she will be closely involved in unmasking Okiya, although the story may only include her in ways that could have easily been written differently to make her irrelevant.
- Vermouth owes Conan again for half breaking her promise to leave Shiho alone.
- Kaitou Kid is officially involved, so he could be dragged back in as needed.
It's pretty easy to start connecting likely dots. If Akai is going to save Shiho dramatically, she must be threatened. Amuro is the most likely threat source because he and Akai need to have a clear fight. Sherry is dead to the Org for now, so the post train arc is going to start on Conan's identity first. Ran, Sera, and Amuro may be involved here. For the plot to get back around to Shiho, it will probably have to go through Conan first to reach her. Maybe Amuro will figure out Conan's identity and then find Shiho's from there, or it will go the other way around and he will see Haibara and guess what happened to Conan. Evidence/news/etc of Sherry still being alive should make it back to the Org to threaten her again. The main problem is if news of Akai does as well, Kir is out. Gosho will have to contrive a way to let information about Shiho out, but not Akai. Conan's absolutely can't get back to the Org at all. Amuro's "soft" personality here may contrive this (echos of Date?) and he will keep their secrets for some reason. Alternatively, Vermouth, to repay the favor, can potentially force Amuro to keep quiet somehow, or even kill him because she has a bad guy license to kill. Akai could also kill him, but I see that as less likely. Amuro has the survived-one-case anti-death plot armor.
TLDR: Used logic to guess the upcoming plot.
[1]Examples of Gosho setting up situations where certain characters were plot-obligated to be heroes...
- Megure "failed" to keep his wife from danger when she was hit by a car while acting as bait. Megure became Sonoko's obligated hero and makes up for the past by getting to her first and keeping her from danger when it reminds him of his wife's case.
- Sato's father's death was set up to be a weak spot for Sato, so she was the one who defeats her father's murderer in a battle of wits. Takagi had an important moment with the case solving and handcuffs because he is obligated to prove himself worthy of being Sato's destined lover.
- In the Matsuda case, we find out Sato loved Matsuda, but he is dead and Sato is angsty about it. The story was pretty much designed to replace Matsuda with Takagi. Naturally, Takagi takes the commanding role in the plot while Sato is mostly useless because she couldn't act strongly without also weakening Takagi's standing relative to hers (and by proxy Matsuda's).
- Yamato cleans up his unsolved mentor's murder that has bothered him personally and kept him from being with likely-destined-lover Uehara in the the Fuurinkaazan case. His spotlight moment is a dramatic armor appearance and fight.
- When Kogoro's cases get personal, he becomes more competent because the plot demands he specifically has to right the wrongs to avoid being a complete failure type. This often happens around Eri because Gosho is trying to show he is still good enough for her.
- Antagonist example: Gin rescued Vodka from Conan's plan in Black Footprint because Conan could not be allowed to gain an advantage over the Black Org yet even though Vodka is "below" Conan's level. Gin specifically stepped in because he is Conan's main rival. (Even though the boss is Conan's Moriarty, that person is still an abstract plot force.)
Shiho+Subaru =betray sister? no cheating 
peace~
