The latest chapter(s) have got me thinking as to whether a person in Sage mode may very well be immune to genjutsu of any form.
First, regarding Itachi, I'm not even sure that he even tried to cast Tsukiyomi on Kabuto, but merely activated his left MS (his Tsukiyomi eye) as a bluff to setup Kabuto for that sequence. I say this in part because he didn't say "Tsukiyomi!" with his MS eye being open, which they (doujutsu users when casting jutsu, especially MS like they have Turret's, lolIn the latest chapter, even though this was a shadow clone take a look at Itachi's eye:
That was Itachi's left eye with the Mangekyuo activated. With Itachi, the left eye casts the genjutsu Tsukiyomi while the right eye is used for ametarasu. He appears to look at Kabuto but to no effect.You must be registered for see images
NOTE: I am aware that Kabuto is shown with his eyes closed in the following page, but this may have been due to the impact of the crows on his body. Also, in the panel shown Kabuto says 'i told you, take your time' and at this point he appears to have his eyes opened if you look carefully.
As well, Kabuto was saying that Itachi should've taken his time because he thought he stabbed him, but I don't see what that has to do with the genjutsu discussion here. Going in, Itachi already knew that Kabuto's eyes were covered by the sclera as well. Here, you can see after he's used that dragon sage jutsu (when he needed the sclera to protect his vision) he's still got the sclera up, at least that's how I interpret the dark band over his eyes. Please correct me if I'm wrong, since I've only read this chapter once and then gone over certain parts as necessary. I don't mind being corrected by you, lol.
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Now, regarding why Jiraiya and not being affected by the frog song genjutsu. I can approach this from multiple fronts. First, it makes no sense plot wise for the caster of the jutsu to have to fear getting caught up in his/her own genjutsu like that unless it's a known risk of the jutsu and an exception to the rule of everything we've seen to date. Physics wise, and not using advanced principles, but basic ones that even Kishi would get, when you generate sound waves like that (i.e. directional harmonic waves - kishi would say directed song or something plainer), the amplitude at the source is basically zero.When Jiraiya uses the 2 Elder toads to cast the frog song genjutsu, why does he himself remain immune to the effects of this illusion? The working of the jutsu was explained here:You must be registered for see links
It attacks the victims brain through their sense of hearing....
That is how the jutsu is explained by the Pa the elder toad, and its used to attack Pain as genjutsu was what appeared to be his only weakness at the time.
Now, why does the song not affect Jiraiya...?
A genjutsu relies on a certain form of stimulation to take effect. It can be induced by looking at some one's eyes(sharingan) or in the case of J man and the toads via sound and attacking the sense of hearing. But what affects one person, surely must also affect the other? Notice here:Look at Jiraiya's hand, its to the side. He does'nt even attempt to cover his ears. But if the song affects any one who hears it, it should also affect Jiraiya, no? Yet it does'nt.You must be registered for see images
Further, because the song, in order to become effective, must combine Ma and Pa's voice it requires their voices to travel some distance from Jiraiya before the independent sound waves of Ma and Pa become cohesive into a singular sound wave that is the frog song genjutsu that affects others. This is likely what ensures protection of the caster, as neither Ma nor Pa alone can do it. While they're right next Jiraiya's ears, the actual frog song genjutsu, which is a synergistic combination of their voices is not synthesized until some safe distance away from Jiraiya moving in a direction away from him. That's really elementary, and enough so, that I believe Kishi would understand that. While I have a book entirely on the subject of the physics of waves, I don't need any of it to explain this or even really more than some basic understanding from a mid/high school text book years ago. To put it into a logical operation, the frog song genjutsu is an AND operation. It requires Ma AND Pa, whereas Jiraiya at the source is getting only Ma OR Pa, an OR operation, which is insufficient. This is math/computer science logic, but it's analogous to what's happening, and really just a way of explaining alternately and more elaborately in less writing why Jiraiya is immune. Thus, there are plot and basic science (i.e. those that Kishi would know) reasons for Jiraiya to be immune that have nothing to do with sage mode.
Next, regarding Shisui's genjutsu, I'm confused why it's relevant here, as it was programmed to trigger when shown Itachi's MS and would definitely not have immunity and be affected. Thus, of course Itachi was the one who was affected, and he did it on purpose as shown here by casting an MS technique on Naruto to bring out the crow with Shisui's eye, that was originally meant for Sasuke who would have Itachi's eye's with his EMS.Just another point:
Some people might say well, the person close to the genjutsu source may have a natural immunity. Yet over here:
Itachi, despite having his Mangekyuo activated and being the person who gave Naruto that eye, is affected completely by Shisui's genjutsu.You must be registered for see images
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Here, Itachi intentionally cancels Kabuto's control by activating his MS while looking towards the Naruto and the crow with Shisui's MS and thus invoking Kotoamatsukami on himself.
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Finally, Itachi explains what he did with the crow and Shisui's MS to break free of ET. The Kotoamatsukami genjutsu command was "Protect the Village of Konoha," which overrode Kabuto's commands, probably simply due to the temporal order of the instructions, as Kabuto believes he can get Itachi back now if I recall correctly.
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Finally, the thing is we don't know what Kabuto's chakra flow looks like right now. If he's mastered absorbing nature chakra in way that's constant then controlling that chakra flow to/from the brain (i.e. "control the chakra flowing through and linking their cranial nerves" according to Jiraiya, see links below) should be possible (this is actually the best case scenario for a genjutsu using opponent actually) even without the ability to use nature chakra I would think. The ability to use nature chakra comes from being able to absorb it and mold it in a way that can be used for nin, gen, and taijutsu. Controlling chakra flow, seems to me separate from actually being able to having to be able to use sage mode or other modes, as it's more of a hands off experience in a way. It's more like traffic control and modulatory action if you will. At least that's how I view genjutsu. What would actually make it more difficult is if the current of chakra were not constant but erratic, stochastic, etc., which is why to break genjutsu one disturbs their own chakra flow or has another do it for them, whether it's a partner in the form of a Bijou, person, Samehada, etc.We all know that genjutsu can be overcome by disturbing one's internal source of chakra. This was shown in the Killer Bee Vs Sasuke fight. Yet what happens when the source of chakra is nature itself, and as such is constantly in change? It would appear as natural energy is used, every time the wind increases/decreases a person in Sage mode has their chakra disturbed. Thus, possibly rendering them immune to genjutsu as long as this state is maintained.
Thus, in summary, I don't think sage mode (either toad or dragon/snake) grants the user immunity to any kind of genjutsu we've seen so far in the manga. However, the only way to prove that is to observe a person in sage mode get caught in genjutsu, until then it's speculation regardless of the argument.
Note for additional good reference material: during Naruto's training with Jiraiya, here is where Jiraiya explains casting and breaking genjutsu (it's actually a flashback to the training while Naruto was caught inside Itachi's finger genjutsu at the beginning of the rescue Gaara arc):
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Peace