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That is on August 27, 2552, during the briefing where they learn that there new mission is to capture a prophet. Dr. Halsey says that Three Spartans are too far away to be recalled, three have died in the last decade, and one is too injured to continue active duty. There is also Sam who was killed in 2525. That makes 25 Spartans out of the 33 that survived the Augmentations without serous side affects.
However on Page 7 of First Strike:
27 Spartans braced themselves
Remember that at this time there are 3 Spartans in space. That makes for a total of 30 Spartans. This is on August 30, 2552.
There is also this from page 276 of The Fall of Reach:
The Elevator doors opened. The Primary Storage bay had been converted in barracks for the thirty Spartans
That is also on August 30, 2552. So on August 27 there were 25 Spartans. On August 30th there were 30. So somehow there are 5 more Spartans than there should be. Even of the 3 Spartans that were too far away to be recalled came back and the one that was too injured was healed, one Spartan shouldn’t be alive.
So how could 5 more Spartans who shouldn’t be alive suddenly appear? The answer is cloning. And Colonel Ackerson had everything he needed to make clones of the Spartan IIs.
Johnson…
In Halo 2 Johnson tells us that how he escaped Halo is “classified.” In Halo First Strike we learn that he had Boren’s Syndrome, which is how he didn’t get infected by the flood. However, there are still gaps in the story, like how he got out of the structure in the swamp and ended up in space with an ODST and a ONI spook. I have an explanation…
Chapter 30 of The fall of Reach is a cryptic message from someone on Gamma station to someone in ONI. It is quoted both here and above:
0000 Hours, August 29, 2552 (Military Calendar) /
narrow-band point-to-point transmission: origin
UNKNOWN; termination: Section Three, Omega secure
antenna array, UNSC HQ Epsilon Eridani System, Reach
Military Complex
PLNB priority Transmission XX087R-XX
Encryption code: GAMMA
Public Key: N/A
From: CODENAME: COALMINER
To: CODENAME: SURGEON
Subject: PROGRESS REPORT/OPERATION HYPODERMIC
Classification EYES ONLY TOP SECRET (SECTION III
X-RAY DIRECTIVE)
/file extraction-reconstitution complete/
/start file/
Secure space-dock repair bay. Corvette Circumference
undergoing final stealth upgrades. Shipyard records suc-
cessfully altered.
Queries detected from transient AI. Operation deemed AT
RISK of being uncovered.
As per contingency plan TANGO: ship registration num-
bers scrambled; hard isolated from dockside computer
network; counterintrusion software implemented; Alpha se-
curity protocols enacted onboard.
Just as you called it, sir. Don’t worry—as far as the sta-
ion computers are concerned, Circumference never
even existed.
/end file/
/scramble-destructuion process enabled/
Press ENTER to continue.
I believe Ackerson received this message. I don't have any real proof, except that the message was sent to ONI, and Ackerson works for them. Also, I think that out of all the characters that we know of, he is the most likely to be receiving this message.
Later on, we find Johnson and 3 other marines on Gamma station. i think that these marines were performing Ackerson's work on the Circumference.
I think that shows that Johnson was working for Ackerson.
In First Strike we Find Sergeant Johnson on a Pelican with an ODST and an ONI agent. Where did this pelican come from? All of the human’s pelicans from the POA except Echo 419 were aboard the Truth and Reconciliation when it crashed into the ring and was destroyed. We know that banshees shot down Echo 419 shortly before the POA blew up. How did he get on a pelican when he was supposed to be aboard the Truth and Reconciliation with all other UNSC personal except the chief?
To find out what happened to Johnson in this time we have to listen to the paranoid marine in the level 343 Guilty Spark. Two of the most important quotes are below.
Play dead! That's what I did... played dead. They took the live ones... oh, God, I can still hear them!
When he says “they” he is not referring to flood. We know this because the flood also takes dead things. The Gravemind took Regret when he was dead, and in the level Keys Cortana says
Look, in the corners. The Flood are gathering bodies.
So we know that he wasn’t referring to the flood. He must have played dead to avoid being taking by someone else…
Sarge? Mendoza? Bisenti? Oh, God... the things took them... <mumbles and cries> They're gone! Get it? Gone!
This is more proof he is not talking about the flood. Sarge was not taken by the flood. However, he was arrantly taken by someone, or something else. My Guess is he was taken by Ackerson’s men.
Here is my idea of what happened to Johnson:
Johnson and a few marines are fighting the flood when Ackerson's men (probably Spartan IIIs) come into the room and kill the flood. They then capture the live humans and take them to their base on the ring. Before halo is destroyed, Johnson escapes on a Pelican from their base.
About the Novels
Some of you that read this are probably thinking that the books and the games are separate, and that the books are just glorified fan fiction. That is incorrect. The authors of the books worked closely with Bungie, and were given access to the Halo Bible, which contains the story of Halo and information about all the events and characters in the Halo universe. They had to follow the story that Bungie had already written and everything they wrote had to be approved by Bungie. There is also this quote from Joseph Staten, Cinematic Director at Bungie Studios.
The books are, for better or worse, part of the canon. In the future we may choose to revise or flat-out ignore some of the less appealing ideas (Johnson's biological immunity to the Flood, for example), but folks should treat them as defining elements of the Halo universe.
And to Eagle 117: Sorry about the title
UPDATE
Chapter 30 of The Fall of Reach(which can be found above. Twice.), mentions an operation HYPODERMIC. This is the cahpter where we learn of the work on the corvette Circumference. In this theory I have speculated that the ship may be a trap, but there is something else interesting about it. Maybe the changes to the ship were the last part of the operation. The Defijtion of Hypodermic is:
1. Of or relating to the layer just beneath the epidermis.
2. Relating to the hypodermis.
3. Injected beneath the skin.
Could the purpose of operation HYPODERMIC be to "inject" something into the Spartan program? Something like 5 clones? Chapter 30 takes place on the 29th, which is between the 27th, where there were 25 Spartans, and the 30th, where there were 30....
You wrote this about Halo2, what does it have to do with Halo 3?
If earth has fallen and has been taken over by the covenant, that is the time for Ackerson to use his Spartan Clones. I think he has his own objective and we may get to see Colonel Ackerson and his Spartan Clones in Halo 3. Ackerson seems to know a little bit about the Forerunner and the artifacts that they leave behind, and I believe that he is definitly up to something. We first heard about Spartan Clones in Halo 1, and I believe that it is possible that we will finally get to see them in Halo 3.