How the duo can counter each technique:
Flying Thunder God Technique: Using the Flying Thunder God Technique requires a massive amount of chakra.
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It took three Jonin’s to perform a single Flying Thunder God technique, when Minato could do the same thing by himself, multiple times. This fact leads us to believe that Minato has a massive amount of chakra reserved to continuously utilize Flying Thunder God. With this in mind, we also know that Kisame’s sword, Samehada, is capable of using an ability referred to as quasi-sensing. This ability allows Samehada to detect opponents with a significantly high amount of chakra. Minato can utilize the marking of his Flying Thunder God technique to avoid attacks, but considering that he has such large chakra reserves, Samehada will sense his presence and inform Kisame of his whereabouts, who will inform Kakuzu, so that the two can target his location and initiate their next attack. The Flying Thunder God technique also allows Minato to mark his targets and teleport to their side near instantaneously at any time he pleases. This will technqieu will not work on Kisame nor will it work on Kakuzu. Kisame, possessing the ability to abvsorb chakra, will just sterilize the marking by absorbing chakra from it and can do the same for Kakuzu. Kisame will know once he is marked, because Samehada will inform him of the foreign chakra present on Kisame’s body.
Flying Thunder God: Guiding Thunder: There really isn’t a way for Kisame and Kakuzu to counter this technique, other than ochestrating a collaborated attack in order to attack Minato while he performs the attack. Under the scenario that Minato uses Guiding Thunder, more than likely in order to combat Kakuzu’s Katon-Fuuton comnbination, Kisame could come by and suprise attack Minato, without putting himself in danger of Kakuzu’s attack, considering his healing factors, durability factors, and chakra-absorbing factors. While Minato may have the reflex and speed necessary to avoid this collaboration, it’s only a matter of time before Minato tires himself out and succumbs to a collaboration such as this, or even a more complex one.
Spiralling Flash Super Round Dance Howl Style Three: Utilizing Kisame’s sensory abilities, they can counter this the same way that they could counter the first Flying Thunder God technique.
Rasengan: Given what was said above, Minato’s rasengan doesn’t have that much destructive power to begin with. Factoring Kisame and Kakuzu’s massive durability feats makes being injured by Rasengan nearly impossible. Kisame himself survived having his ribcage blown out
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by an attack arguably much stronger than a base rasengan, and immediately healed from the damage. He even survived Hirudora
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whose explosion dwarfed the massive “Turtle Island” and was supposed to be a one-shot kill. He even had enough strength to potentially move his limbs afterwards, to which in reponse Gai punched him.
Kakuzu’s most notable feat was the very fact that his body was kept intact after being hit directly by a Rasenshuriken.
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And even though he did die, it only goes to show the durability of his body and its ability to endure a technique that causes damages on a cellular level, attacking the chakra circulatory system to such a degree that no amount of medical ninjutsu can heal it.