So, lets refer to the original orders given to the team by Danzo (important quotes in bold font):
"I am Shimura Danzo," he said. His one visible eye swept the crowd of assembled shinobi sternly. "Many of you are too young to know of me. That is fine. I have mentored some of you. That is also fine. That you do not see the Hokage standing before you does not make this any less of a village emergency. Twenty years ago we had five times our current numbers and still lost over a quarter of those shinobi to this blight. Not only will you have fewer in the way of numbers, you are commanded to do so speedily before the…" his nose wrinkled like he'd tasted something foul, "visiting Villages come to suspect anything."
"In your favor is this: when last we fought the Chakra Orchids, it was during a time of war where we did not have the luxury to choose our soldiers, nor did we understand the enemy we faced. Today we do. It takes over bodies: very well, you have all been tested and vetted, you will not succumb to the infection. It uses the bodies of the infected to spread its infection: so be it, we will let none escape. It is smart: that means we will not underestimate it. You are all veterans of some standing or candidates promising enough that very senior ninja have recommended your inclusion in this mission. It is A-ranked and will be remunerated accordingly."
"Symptoms for those that have been parasitized are as follows: a cough, followed by fever, pain, delirium, death. A flower then blooms, usually at the base of the neck and the body now a part of the chakra orchid hivemind. The varieties we know of are as follows: the blues are workers, the whites warriors, the reds seed-bearers and the silver the leaders. All should be mere wildlife at the moment and as such they matter little next to our main concern which must be the main plant which is gold and often heavily defended. No doujutsu has ever managed to seek it out and so we are left with covering ground the old-fashioned way. Identifying and destroying the main plant is your priority. Root it out and burn it to nothing."
So the TL,DR version of the original orders was to eliminate the golden orchid before any of the other villages' representatives notice. This is a time sensitive seek and destroy mission, and the team has wasted lots of time already waiting for reinforcements.
So question 1: Is the team mission capable? Yes, it is. Shino is down an arm and some of his bugs, but that can be worked around. The team would have to deploy assets to protect him, but he is not a liability and can support the front line from a distance.
Question 2: Can we fulfill the team's duities to perform a mission update? Yes. We have Naruto.
Question 3: Is the team capable of destroying the main plant? I think so. Naruto should have explosive tags on him. If he already used them though, the team probably doesn't have the firepower to bring down the plant.
Question 4: Is the team capable of getting through the golden orchid's bodyguards? Perhaps, with a little subterfuge and distraction.
Question 5: Are we playing in a shounen manga world? Is this Exalted? Yes. Rule of Cool then:
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[x] (Stunt 01) "Naruto, do you still some explosive tags left?"
-[x] If the answer is no, retreat and find reinforcements
-[x] If the answer is yes, then say, "The mission is time sensitive. We are going to enter the tower. Here is the plan..."
--[x] "Alright!" Naruto announces after hearing Hinata's plan. "Lets get this party started! Kage Bunshin no Justsu!" After a giant cloud of smoke, eight more Narutos appeared. "You, you, and you," Naruto says pointing to three different Narutos. "You guys are on message duty. Go get us some help." The three 'messenger' Narutos nod simultaneously, and jump toward the trees looking for a chunin or jounin to report their status.
--[x] "After the Narutos assigned message duty leave, the real Naruto announces, "The rest of you, you know what to do." Two of the Narutos immediately Henge into copies of Hinata (in human form) and Shino, and head to the trees. They find a good hidden location to form a "firing line", then two of them loose their kuni with explosive tags at the monsters on guard duity while the rest throw regular kunai. KABOOM! A mix of plant splinters and animal giblets fly away from the explosions as a few of the monsters die and injuring several others. "Oi! Come and get us you overgrown pile of monster dung!" a Naruto clone yells out to the camp of monsters, while turning his back and spanking his butt. The other clones subsequently throw another set of kunai, one of the kunai with another explosive tag. KABOOM! With a cry of anger, most of the animal/plant hybrids give chase to the Naruto clones, who are running off away from the real group, leaving only a skeletal force of guards for the golden orchid.
[x] (Stunt 02) If the group of Naruto clones was successfully able to draw most of the guards away (verifiable with the Byakugan) in such a way that they can't quickly return in time (say, a few minutes), begin the attack on the plant monster. If they were unsuccessful, retreat and find help.
--[x] "I think they are far enough away now," you say. "Naruto, remember to avoid doing chakara intensive jutsus. We need you to be fresh when we take on the orchid." Naruto nods. "Kage bunshin no jutsu!" Several more Naruto clones appear, and all of them take a defensive position around Shino.
--[x] After you get into position, Shino launches a surprise attack at the defenders with his bugs, catching them unawares and devouring their chakara. With a cry, you attack. Pushing chakara into your wings and shaping them a certain way, you turn them into psudo chakara blades, cutting whip vines and animal legs with equal ease. Like water, you flow around their attacks, always moving, never stoping. You see a vine try to catch your legs. With a nimble jump and a beat of your wings, you fly over the attack, beheading another monster as you fly right by it. Shino watches your back, supporting you from the rear, while Naruto and his clones engage any beast that gets close to Shino.
---[x] If the team can't defeat the monsters within a minute or so, disengage and retreat. The golden orchid will undoubtedly recall all the infected beasts that were chasing the clones, and we can't fight both the giant plant and his minions at the same time.
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I think that is enough to get through the next update. My personal plan for the final boss is to have Shino and some Naruto clones hold the rear while Hinata and the real Naruto assault the boss. The real Naruto and Hinata would be the distractions, while the clones get into position to encircle the plant. The main emphasis would be to always have the ability to disengage with Hinata guarding Naruto and Shino and a few clones outside keeping watch and making sure our escape isn't cut off. Killing blow will likely be from a bunch of Naruto clones letting loose a bunch of explosive tags on the boss at once. Also, I'm not familiar with Exalted powers at all. If anyone has improvements, go ahead and write them in.