Watching this again with the commentary (which is pretty good btw), and listening to the ideas behind the film I thought of how I'd have the final act play out after Shingen is defeated:
- Mariko arrives at the lab, where she discovers that Yashida is alive but comatose. Fearing that he was becoming too weak, Viper had to put him in this state to keep him alive.
- Logan heads for the lab and fights the ninja clan. He is eventually overwhelmed and captured.
- With Logan contained, Harada and Viper argue about how to proceed. She reveals that she is close to perfecting a formula for immortality based on Logan's DNA already, but wants to hang on to Logan for further testing. She claims to have associates interested in the product. He leaves, unsure of the deal he's made.
- Harada visits Mariko in manner similar to the film. He tries to convince her of the honour in his acts, and to let go of Logan. Meanwhile, Viper taunts a still-discombobulated Logan about his failures, explaining how he's about to become a lab rat again.
- Mariko lures Harada into a kiss and stabs him in the leg, running off to find Logan. He catches her up quickly and aggressively tries to win her over. He tells her he was destined to be her guardian but she blasts back that she can only trust Logan to be there now. He appears broken, and allows her to leave.
- Yukio breaks into the lab and engages in a fight with Viper while Logan tries to break out of his shackles. As Logan yells, Yukio rampantly destroys Viper's lab whilst parrying her attacks. Their fight travels out of sight and we're left with Logan, alone in captivity.
- Mariko is running through the lab corridors and passes Yashida's room. She enters and wakes her grandfather, where to two have an emotional conversation. Yashida confesses that he is scared to die, and she conforts him as he passes.
- Back to Logan, and Harada enters in full Silver Samurai armour. He is beside himself with anger, and releases Logan for a duel to prove who is a worthy protector of the Yashida family.
- Still fighting through the labs, Yukio deals what she believes to be a deadly blow to Viper, but is shocked when she simply rises to her feet again. Peeling away damaged skin with her fingers.
- Logan and Harada's fight continues, with Harada screaming about honour and purpose. He recants living in the shadow of the Wolverine, and how Logan has supplanted his clan as the mythical guardians of his people. Taking the upper hand, he draws a special sword out of his arsenal, which he explains can be super heated to cut through even adamantium. The fight picks up its intensity with Logan desperately dodging the deadly swipes. He can only resist for so long and Harada lops off the claws from Logan's left hand in one swing. He recoils in agony.
- Yukio is running out of steam against Viper, but just when it looks like she is about to be taken out, Viper is struck with a dagger from out of screen. Mariko appears and hurls another blade into Viper's chest. Seizing the moment, Yukio springs to her feet and lands that awesome killing move she uses in the film.
- Logan stumbles around trying to defend himself but is still weakened from the poison and wounds. He loses his other set of claws, collapsing to the ground. Here he lays, near death, and has one last visit from Jean. She tells him it will be over soon, and that he wants this. Logan refuses to die, he's grieved enough, he wants to live. Ducking Harada's swing, Logan bursts up and knocks him to the ground in pure, animalistic rage. The superheated sword falls away, and Logan's claws regrow in bone form. Harada pulls another blade with haste, and the two charge at each other, dealing deadly damage, only one will recover.
Then the rest plays out the same.
