Things didn't develop differently from the Movie. Naruto and Kushina protected Sara, and Sara realized that "Anrokuzan" was Naruto's target.
With a series of incidents, she realized the minister's true face, and decided to help Naruto defeat him.
On Minato's side, the others also located Anrokuzan with Shibi's abilities. When they arrived, they found that Naruto and Kushina had already joined forces to defeat their enemy.
Anrokuzan made himself a giant body of a centipede with his puppet army and the Ryumyaku's powers. His true body however was hidden within, maneuvering his new form.
Kushina and Naruto were mother and son, and their fighting styles were very similar, with both relying on their immense Chakra to crush their opponents.
But their joint attack was no good enough. Because Anrokuzan had absorbed the power of the Ryumyaku, he could regenerate indefinitely, and was not afraid of being hit by their attacks.
Minato joining the two didn't have an effect as well.
Shibi wanted to help, but he was stopped by Ryo. "Shibi san, this is a family fighting together. I think we outsiders shouldn't interfere."
Shibi hesitated a bit then nodded.
With Minato's presence, Kushina was more open to attack, and Anrukuzan's movement was somewhat restricted.
With Kurama's power, Kushina was really destructive in her Three Tailed Coat Mode. His puppets were quickly smashed by her brute strength, and his main body was exposed.
Naruto and Minato together formed the Supreme Ultimate Rasengan, and at the same time, Sara Closed the Ryumyaku. With that, Anrokuzan wasn't able to regenerate as before. The Supreme Ultimate Rasengan hit his main body, destroying him completely.
With that, Naruto was able to defeat Anrukuzan with the help of his parents. But that wasn't the last thing to see from this enemy. With his last breath, he made his body fall into the Ryumyaku, causing it to erupt.
As in the Movie, Minato had to seal the Ryumyaku immediately, which meant that the time had come.
Kushina was reluctant to let go of her son after remaining with him for so long, and Naruto's eyes always stayed on Minato.
After all, he had been with him mother his whole life, but his father was a missing figure throughout his childhood, with only a few pictures, and an engraving of him on the mountain remaining in his life.
Feeling Naruto's gaze, Minato smiled at him, and then put his Kunai through the floor, sealing the Ryumyaku.
As the Ryumyaku was sealed, Naruto and Yamato's bodies started emitting light; they didn't belong to this time.
Kushina and Naruto said their farewell, and Yamato took the opportunity to retaliate against the kid Kakashi who had bullied him, hitting him in the head.
"Why didn you hit me?!" Kakashi raised his head and looked up to Yamato.
"Well, I've been always bullied by you, so there you go!" Said Yamato with satisfaction.
Minato did not participate in this conversation, as he prepared to seal everyone's memories. Ryo wasn't worried, as he should only erase these memories, not the ones he previously sealed after talking to Kurama.
The white light on Naruto was getting brighter, and he realized he was about to leave. He couldn't help but say something to Minato, but the latter interrupted him.
"It is my pride to have a son like you. We will have a chance to talk in the future. See you again!" With his voice falling, Naruto and Yamato vanished.
(Author Note: I did not focus on Sara's emotional interaction with the characters, as these events are mainly a preparation for what's about to come.)
After Naruto and Yamato disappeared, the rest of them looked around puzzled, not knowing what was just happening. Minato sealed off all their memories of what happened in Roran, and all they remembered was entering the city.
Kushina forgot everything leading to the incident, and looked up awkwardly.
"Minato, Ryo, Ryo Kakashi, what are you doing here?"
"Kushina, what are you doing here?!" Minato was shocked by her presence.
She repeated the same explanation, and her promise to Ryo of returning to the village was obviously forgotten.
Under the blend of Kushina's love and wrath, Minato could only agree to take her along with him to the Lightning Country battlefield, and at the same time, he decided to go the Konoha, in order to report to the Hokage.
After looking around, Ryo saw Minato's seal, and immediately understood where he was.
Minato also understood after seeing the seal that the task should be done with, and understood that memories involving any details about it were completely sealed.
After Minato explained the situation, he apologized to everyone for sealing their memories. Of course, with none of them recalling anything, they had no complaints.
With this, Roran's mission ended, and Minato sneaked out with his squad and returned to Konoha's camp with Flying Thunder God.
No one noticed that Ryo had left a Shadow Clone behind.
The purpose of him doing that was to check out the Ryumyaku's power. Soon after being sealed, Ryo sensed that the Ryumyaku still had some of its power still within some of the puppets outside.
He didn't want anyone to know, so he secretly left his clone behind.
When perceiving the Ryumyaku's power previously, Ryo noticed that it had a special Chakra. While it was part Natural Energy, it was mainly closer to regular Chakra. Still, it was somewhat similar to Senjutsu Chakra.
Anrukuzan, previously named Mukade, used this power to achieve a quick self-repairing effect. Ryo wanted to know whether Anrukuzan's method caused those effect, or the whether the Ryumyaku itself had those properties.
The clone had half of Ryo's Chakra. Ryo's idea was trying to collect this energy from the puppets. If all goes smoothly, the Clone could just travel to the Lightning Country. Otherwise, it would just go to Sakumo's camp, as it was the closest to Roran.
Things went unexpectedly smooth. With Anrukuzan's death, the puppets were inanimate.
It was easy for Ryo's clone to collect the Ryumyaku's energy from the puppets and seal it within a scroll, and then go directly to the Lightning Country camp.
After Minato returned to the camp, he asked Ryo arrange a residence for Kushina, while he used Flying Thunder God to go to Konoha and report to the 3rd.