Update Addendum
Benethrezim had prepared extensively for the anticipated Soltyrian invasion. One of their plans was to yet again strike a blow at their enemy from the inside. This particular mission was assigned to Solid Snake: To enter Soltyria and blow up the Academy of Nature. The Academy of Fire was already accounted for through the fire symbols inprinted by Seth Dethos. The mission went very well, until something rather unusual happened (read: until Reno sent his orders)

Observe:
As the sun breaks above the ground, an old man stands on the hill. As the ground warms to first to the first rays of light, a singing bird shatters the peace and quiet. Igor, a deformed servant who Seth brought under his care was bringing him a letter.
Igor: Master, the Soltyrian Meatbags have sent a reply on your demand to return the Fire Academy.
Seth: Give it to me.
Seth was reading the letter. He seemed displeased, very displeased. His eyes went ablaze, you could see a madman in his gaze.
Seth: Pathetic maggots, I nearly destroy my arm by writing hundreds of books and now they treat me like this. They shall be consumed by the fire they sought to control. Bring Snake to me.
Igor: Yes Master.
Later that evening in the Tower of the Great Satan(Seth's residence)...
Seth: Hello Snake. I invited you for a little chat.
Snake: Invited. That's what you call sending armed troops to my home?
Seth: Apologies if they were rough on you. But the time is short, and I have a mission for you.
Snake: Cant you send my father? He is the Big Boss.
Seth: Yes, about that your father has gone bat sheet insane.
Snake: What!?
Seth: A vampire from the Malkavian clan used his Dementation powers on the captured bandits to drive them insane and thus somehow increase his oracular capabilties. Your father bravely brought the bandits in himself and was acidentally caught in the spell.
Snake: The old man and me grew apart, but I'm still sad that he has gone mad.
Seth: The Malkavian who is insane by his bloodline, told us very cryptic things. He said that the Shaemar are building gadets he described as 'boomsticks'. The Soltyrians dream of perfection, a grand Ark that will deliver their people to salvation. Rollux is covered in darkness,but seeking union with the Zombie Masses. The Masses themselves are also seeking to unite and eager to start their unholy crusade.
Snake: Strange. Where is my father now?
Seth: He is in my personal residence, The Tower of the Great Satan. He spends most of his time running around, calling himself Jack Bauer while waving a crossbow and yelling "WHERE ARE THE PLAGUE VIALS!?"
Snake: I'll have to pay him a visit soon. What is the mission?
Seth: I want you to infiltrate the Nature Academy in Cha'dra.
Snake: Cha'dra!? The Capital of Soltyria?
Seth: Yes. This here is an explosive orb of fire magic. Crafted it myself, this very day. Expensive little thing. I have dubbed it the Academy Buster. You will place it inside the Academy and detonate it.
Snake: While I am in inside?
Seth: No. It has an magical clock you can set, you will determine the amount of time you need to get out. Dont worry though, once its activated it cannot be disarmed or moved from it's position.
Snake: Right. What is the method of infiltration?
Seth: Naval, sort of....
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Sunrise. The Soltyrian advisors were getting off the ship. As promised they were sent back home by the next decent available travel ship. They were picked up by the government and taken away. Another man got off the ship as well. He wore a simple light green robe and hood, and seemed frail and weak. He carried with him a small travel bag.
He went off to the main square, and purchased a ride to Cha'Dra. Real baragin. Soon the wagon filled with lots of other people who needed a cheap tranport to the Capitol was on the way. The crowded wagon travelled along a bumpy road, which annoyed him. He took out a roll of paper and some kind of leaves. He crumpled the leaves and put them on the paper, then he rolled the paper into a cylinder. Igniting one end of the cylinder with a torch that is used to illuminate the path ahead, he put the cylinder in his mouth and inhaled the smoke it produced. Many Soltyrians were unfamiliar with what he was doing and seemed curious, but he didnt care.
A few days later...
The stranger was awaken by a dreadful voice, it was the wagoneer shouting "Wake up folks, we are nearing Cha'dra." several times over. They approached the city gates, the wagoneer handed a list of passengers to the Royal Guard. upon inspecting it, the guards eye focused on a certain name and his face showed suspicion and caution. The stranger heart started to pump faster as the guard quickly leered at his pals and noded. Before he knew it, the Guard jumped on the wagon grabbing one of the men and throwed him out of the wagon onto the hard ground. "We got you scum, thought you could sneak in, didn't you?"
After a small beating to eliminate any possible resistance the man was taken away. The head guard turned to the wagoneer and welcomed him into the city with a smile. "The rest of them are okay, the man we took is wanted for murder. Head right into the city. "
That was too close for comfort, the stranger thought to himself. The wagon entered the city.....it was magnificent, grand architecture and lots of plant life, it was like a Garden in Heaven. It stopped and the passengers got off, the stranger wanted to light up a smoke, but he thought it was best not to cause to much attention.
...
Night fell on the city,it was almost midnight and most citizens were sleeping except the many guards. The stranger was hiding in the dark corner of the Royal Barracks, still in his light green robe and hood. No more. With one swing of his arm he disrobed himself...showing his sleek black sneaking suit. It was none other then Solid Snake. He had information that a wagon of unspecified supplies was going into the academy, currently it was being getting searched at the Barracks for any dangerous items. Everything that entered the Academy had to be searched and cleared for entry. The Soltyrians didnt take any chances after their Fire Academy was destroyed, again. They were done searching it and it was about to continue its trip. Snake had to act fast. He knocked on the nearby wall making a distinct sound, the guard heard it and went to check it out. The guard looked around but couldnt see anything, until he looked down that is. On the ground were erotic drawings of hot female slaves. The guard feel on his knees an started to drool over them while inspecting them closer. Snake used this to sneak on the back of the wagon,it seemed it was carrying fruit and other kinds of perishable food. Snake took one of the boxes and put it over himself. It was the perfect disguise. Who would suspect a box? The wagoneer returned and he continued to the Academy.
...
The ploy worked,he has passed the Academy gates. He peeked out of the box and saw nobody but the wagoneer, the air was clear. He silently jumped out of the moving wagon and scanned the area. He was amazed, the Academy was even more beautiful then the city. It was like the Garden of Eden, times ten. The city aqueduct was passing through the academy grounds, again the architecture was supreme, combining stone,water and nature in all it's glory.
He crawled and sneaked through the wild plant life the Nature Adepts made, it was almost like a jungle which played in his favour. He felt sorrow because he had to destroy the knowledge that could be used for the betterment of mankind,but orders are orders and Soltyrians brought this onto themselves.
Snake made it to the Academy undetected, he prepared his grappling hook (
http://www.nationaldefenders.com/ima...pplinghook.jpg) and he launched it towards the window. Success! The hook attached, he steadied himself and started to climb. The climb was exhausting, but he made it inside the Academy. It looked like he was in the stairway between the first and second floor. He needed to get to the ground floor to set the Academy Buster. Snake unsheathed his knife and proceeded downstairs. The Academy was eerily empty, most of the students sleeping in their dorms. However he could hear a guard approaching, Snake hid into the shadow and leaned against a wall. The guard passed him by without even a slightest clue, Snake leaped towards the guard, grabbing him and breaking his neck in an instant. He hid the body and hurried downstairs to the ground floor. While running down the stairs, he bumped into a sleepy guard. The shocked guard tried to punch Snake, but Snake stopped the guards fist with his hand and slashed the guard across the throat with his knife. The guard feel on his knees, blood squirting from his neck. It lasted for several moments and then he completely collapsed on the floor. The blood was everywhere, he couldnt hide it. DAMN! Snake rushed to the ground floor, he crouched and started to set the Academy Buster on the wall. He was just about done,then a pair of guards spotted him. They were too far to quickly neutralize them and they would sound the alarm. He had no other choice. He set the AC to expode in 5 minutes, the clock has started. The guards shouted, waking up the whole academy and have turned to Snake.
Snake: This building now contains enough magical explosives on its key structural point to turn it into a smoking crater. You can still make it if you run.
The guards looked at the AC, then they looked at each other and ran away. He was in luck, smiling he headed towards the exit as well, but suddenly the gate was covered with overgrown plant life. It was the work of an Nature Adept who was awake. Snake turned around and ran upstairs hoping he could make it to the grappling hook. He ran like crazy avoiding the vines and other diabolical spawns of nature the adept flinged at him. Alas Solid Snake was a legend and he was too fast for the adept. Snake got back to the stairway between the first and second floor, he grabbed the rope and started to rappel down the wall. He almost made it fully down whe the Adept caught up and saw the hook, he cut off the rope making Snake fall down from a small height onto the hard ground. ERRRGH! He got up with a growl of pain and ran as far as he could through the heavy vegetation. The Nature adept was watching him from the window steaming with rage.
Tick tock tick tock, the clock goes, tick tock tick tock , the clock goes 3, 2, 1...
A blinding bright light shined from the orb. A huge blast ensued, blowing up first the ground floor and climbing up to the last level of the tower. A huge shockwave erupted from the orb expanding outwards completely obliterating the first floor, it continued on even catching up to Solid Snake. The blast winds launched Snake towards the aqueduct, sending him flying through the air.
Snake: *manly yell*
Through incredible luck he landed straight into the aqueduct, Snake was floating in the water too exhausted to climb out. The water in the aqueduct carried him out of the capital city and into safety.
Eventually after traveling god knows how many miles he managed to swim out of it and get on solid ground. His arm was broken, but he was alive. David knew that an ordinary man wouldnt be standing now. Picking himself up he retreated into the shadows of a nearby forest, to heal up his wounds as much as he could and then proceed to the extraction point where a varactyl was waiting for him.
In the ruins of the Nature Academy, the rescue crew found a strange card in the hands of dead man.
http://img50.imageshack.us/img50/4121/pwned5lp.jpg
...except the ruins did not contain the Nature Academy, which had been recently evacuated. This was also the reason the security was so slack to allow Snake entry in the first place.
After a long and desperate pursuit by the coast with Snake's varactyl ending up getting killed by Soltyrian Wardruids, the daring agent was captured and transported back to Cha'dra for interrogation. The fact that he left his card made it quite easy to identify him.

Now Solid Snake silently awaits his judgment. While eating drugged Kentharu-brand cookies.