RYU GA GOTOKU ISHIN
Ryu ga Gotoku Ishin (released in Japan in February 2014) is a spin-off game set at the end of the Edo period of Japanese history (known as the Bakumatsu period), a period when the Tokugawa Shogunate came to an end and imperial rule was restored (Meiji Restoration).
Sakamoto Ryoma is living undercover, with a false identity, as "Saito Hajime" in Kyoto. One year earlier, on the eve of the coup d'état of Tosa, Ryoma's foster father, the man who raised him, was murdered before his eyes. The only lead he had to discover who the killer was is that he used the Tennen Rishin style of fighting. This is a style used by the Shinsengumi, so Ryoma infiltrates their ranks, becoming captain of the 3rd Shinsengumi unit, in attempt to find the killer.
Big thanks to Kevin Debrabandere for creating a PDF for the entire Ishin guide. You can download the PDF version of the guide here. Please be advised that the PDF is outdated now, but still contains information for the whole game.
This guide is for the original (2014) release of Ishin. The information contained within may not necessarily be accurate for the 2023 "Like a Dragon: Ishin" remake.
Chapter 13 - The Assassination of Sakamoto Ryoma

The chapter starts with Ryoma, Hijikata, Nagakura and Okita sat around discussing what they do next, now that it's basically just them left since most of the Shinsengumi soldiers went with Ito to his new group and it'll be impossible to keep the Shinsengumi going now. After talking for a bit, Hijikata invites Todo into the room, to the surprise of Okita who thought Todo had betrayed them! Hijikata tells them that Kondo's "Final Plan" is to use Ito to bring out the fake Sakamoto Ryoma from hiding. Hijikata explains that they knew all along - from the moment Ito joined the Shinsengumi - that he would try to usurp the group and Kondo has been keeping an eye on what guys he joins forces with, to find out who the Shinsengumi's true enemy is. It turns out Kondo was using Todo to keep an eye on what Ito gets up to. So Todo is pretending to be on Ito's side to find out who Ito works with. Todo tells them the man he's been working with is "Sakamoto Ryoma" from Tosa and coordinated meetings with Katsura and Saigo from Choshu and Satsuma with the aim of starting a huge war across the country. However, the fake Ryoma's true objective is to use the power of the Imperial party to force Satsuma/Choshu and the Shogunate into a war which will leave them in ruins, so he can profit from it. Todo says he doesn't know where the fake Ryoma is right now, because Ito hasn't told anyone, but he says if a meeting is arranged between Satsuma and Choshu then the fake Sakamoto Ryoma will be there. Real Ryoma says they have to try to force a meeting between them, to bring Ryoma out. Todo says it will be difficult, since Ito has his guys out roaming the streets and they'll attack Ryoma if they see him and there's always a chance Todo will be exposed to Ito. As they sit there wondering what to do, Nakaoka shows up, saying he's returned from Tosa, and he's with Oryo and Otose.

Oryo, Otose and Nakaoka take them to her new inn in town called "Omiya". Because of what happened, Terada Inn can't be used at the moment, so Otose set up this place. She tells them that, since it's new, it's not known yet, making it an ideal hideout for members of Tosa, Satsuma and Choshu. She tells them they can do what they want with the place - burn it to the ground if it'll help them! Ryoma asks what she's up to and she explains she wants Ryoma to save Kyoto - she says everything will come to an end if this fake Ryoma is gone, so she's doing what she can to help. Ryoma tells her he will bring everything to an end right here at Omiya.
Now that the stage is set, they need to figure out how to get Saigo and Katsura to meet here. Nakaoka says he'll take care of Saigo - he apparently met with him before and got a picture of the fake Ryoma, which he shows to the others. He asks Ryoma if he recognises the man and he says he does - it's Takechi Hanpeita! Oryo adds that the man in the picture is the same "Sakamoto Ryoma" she knows. So Nakaoka is going to try and talk with Saigo, then Ryoma mentions that Katsura hangs out at his bar Matsunoi in Fushimi, so Todo says he'll head there to try and get hold of him.
After all that, you finally have control. You start in your room at Terada Inn, where you can freely change the time of day by examining the bed, if you like.
First, go back to your house in Another Life. Then leave and go return to Fushimi. Ryoma will say it's time to go back to Terada Inn, so head back to your room in Terada Inn and speak to Nakaoka. Ryoma asks what the update on Saigo is and Nakaoka says he'll be coming along, so they just need Katsura to agree to it. They are about to head out to Matsunoi together to see what's taking Todo so long, but then they hear a noise from downstairs. They rush down to find Todo badly injured - it turns out Takeda found out about Todo's betrayal and attacked him. Todo tells Ryoma to hurry over to stop Takeda, before he reports everything to Ito. Ryoma asks Nakaoka to go to the Shinsengumi HQ and tell them about what happened, while he goes off to face Takeda.

[1]
Go here and Ryoma finds Takeda. After a brief talk about how Takeda is a scumbag, the two of them fight.
After Ryoma defeats Takeda, Okita, Hijikata and Nagakura arrive with Todo's body. Apparently, when Todo joined the Shinsengumi, this is the place where he said he wanted his body to be taken, in the event that he died. They then declare that everything involving this other Sakamoto Ryoma has to come to an end tomorrow night - at Omiya.

Next, we are back in Ryoma's room at Terada Inn. Ryoma says this fake Sakamoto Ryoma will be lured out of hiding at Omiya tomorrow night, so he should get himself prepared for the raid.
When you are ready to go to Omiya, examine the bed and select the FOURTH OPTION. Be prepared for a long fight sequence.
As Ryoma is heading downstairs, Ikumatsu barges into Terada Inn looking for Ryoma. She delivers a message from Katsura - he says he will definitely be at the meeting at Omiya!
Next, we see Katsura enter a room with Saigo sat inside. It seems they are both here out of curiosity over the whole "2 Sakamoto Ryomas" tale. Then, Nakaoka enters the room and joins them, where they sit waiting for "Sakamoto Ryoma"'s arrival. Another man then enters the room, but his identity is not revealed.

After that, we see Nagakura and Hijikata outside, waiting for their signal to move. After the signal, they move into position and raid the building. Then we see the game's opening cutscene again, but from different perspectives this time.
After Ryoma rushes upstairs, you have control again.

As usual, yellow dots are items you can pick up.
[1]
Make your way clockwise around the map to get to the stairs.
When Ryoma gets upstairs, it continues on from the opening cutscene, where he kills this other "Sakamoto Ryoma". Nakaoka tells Ryoma that it turns out the enemy saw through their plan and used their own trap against them! The Mimawarigumi have the place surrounded; Katsura and Saigo managed to escape, but Nakaoka didn't get so lucky. Then Ryoma turns and sees Takechi Hanpeita standing alongside Sasaki and Ito. Hanpeita says Ryoma must have a lot he wants to talk about - such as why he had Yoshida Toyo killed and why he'd been using the name "Sakamoto Ryoma". Ryoma, upset and angry with Takechi, has a speech about why things had to end up this way and how he hates him for this - hates him so much he wants to kill him - and then lunges at him with his sword, but Sasaki and Ito stop him. Takechi tells him he has one "final job" he needs Ryoma to do. He leaves, telling Ryoma he will be waiting for him at Tosa and that everything will be clear to him when he comes. After the 3 of them are gone, Hijikata, Nagakura and Okita enter the room. They see the body of (fake) "Sakamoto Ryoma" on the floor, but they see that it's not the same man as the one in the photograph they saw. Okita asks Ryoma what the hell happened in here. Ryoma, being as cryptic as he can, tells them the man called "Sakamoto Ryoma" is dead - he just died right here in this room.

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