Storyline

Storyline:
'''Please note before you read this that this is simply my take (Gunsrequiem) on the entire Pizza Code Mystery story, and is not something that should be considered set in stone by any means. Hopefully, by highlighting some key points and putting my personal spin on them, it will incite some ideas.'''

So, without further ado, here it is:

I think it has become rather obvious that Dr. Horn set up the HALOS project in the X01 and X02 rooms of the BMRF. As we can see from the letter on Welsh's website, only Dr. Horn, Paul Bottomley, and perhaps Dr. Junek had access to the HALOS project. Furthermore, Horn was using the lab budget to buy pizzas and fund the project. In an attempt to get back at Dr. Horn, Welsh and some of his buddies decide to play a prank on him by taking his pizzas and hiding them throughout the facility.

Before we get to that, however, it's important to understand what we can about the HALOS project. It is definitely some sort of artificial intelligence--we can derive that from a number of sources: That said, the HALOS project is definitely a very crucial entity to Dr. Horn, and it seems as though the HALOS system is still in contact with Dr. Horn after he "escaped" the BMRF.
 * The whiteboard in "Anomalous Materials" that has a note directed to Paul Bottomley that asks him to call J.D. Marcel on ext. 1187-463 about the Niobium-5 that he needs for that "AI project 'thing'".  It is signed "Dr. Montero"
 * The Tempus omnia revelant page added to the wiki has a section that shows a report with the author as {HALOS AUTOMATED}
 * The messages sent out by "someone mysterious" are probably partially sent out by the HALOS AI, particularly because of the way they are worded.  They sound very machine-like and inorganic.

So what about the relationship between Horn and Welsh? Well, apparently Horn got pretty pissed off that Welsh was taking his "misbegotten goods", as we can see from the image attached with the wiki page that Horn scribbled all over in red. He writes, "Stone will pay" and "Steals it, eats it". Either Horn really loves his pizza, or he is pissed that his secret funding is a bust. My money's on the latter.

When all hell breaks loose in the Black Mesa facility, Horn gets out. Paul Bottomley is dead (or is he?), probably killed by the military. Everyone else is running around like chickens with their heads cut off. Horn knows he's the last man standing that can continue the HALOS project--so, what does he do? He activates the AI project, basically giving it the option to fend for itself.

This is where the IRC chat clues come into play. I believe these are coming from someone in an attempt to give Horn directions and aid him in setting up another HALOS site. The second IRC chat clue points him towards Niobium, a vital ingredient for the HALOS project (as we saw on the "Anomolous Materials" whiteboard). The third clue states that the 41Nb was recovered and that the HAFB was compromised. Perhaps this is Horn sending this message to the secretive individual that sent the first message. However, it's important to note the Tempus omnia revelant wiki page that mentions "...Sending MINDAT via HAFB". Either Horn or the HALOS AI was sending mineral data via the Hollomans Air Force Base.

In the same clue that identifies HAFB as being compromised, the message identifies the White Sands Missile Range as "no longer viable", then suggests that the message's receiver move to the main site. The next IRC chat message then states that access was detected at the personal site, the security therefore compromised. It identifies the HALOS project as being under threat, then states that the site is offline as a response. There was an embedded message as well:

prime site compromised return bmrf login halos

The next message definitely appears as though it arises from an AI, for it is in all caps and is attempting multiple methods of attack--it also appears to be attempting to connect to Horn, as it says, "ATTEMPTING CONNECT TO USER H . . . ."

Finally, we are left with the message left for Dr. Horn (by whom?) that reminds him of the password "BENALOHPAILLIER" in case of emergencies. And, as we know, there has obviously been a serious emergency. It also says, "You should bring pizzas", which means that the person (or thing) sending this message was part of the original HALOS project at BMRF, which then identifies why Horn had to buy so much pizza. Whoever was helping Horn with the HALOS project seemed to love pizza, which makes me wonder if the strange messenger is in fact Paul Bottomley. They were working together at BMRF, so it makes sense that it would be Bottomley.

And then we come to the latest clue. It appears to be sent by the HALOS AI, stating that the primary site is offline and the primary servers are overloaded. It then mentions that a user activation is required--PASSCODE INPUT FOR SITE ACTIVATION REQUIRED, and the final test pattern has been set.

So, alas, this is where we stand. BMRF is toast, completely annihilated by the combination of forces Gordon Freeman had to deal with. Horn is on the run, perhaps holed up in some remote location attempting to get back into the HALOS AI program, or even attempting to reroute it to his current location. The message left by Bottomley about bringing pizzas suggests he is still alive and still in contact with Horn. Welsh is holed up somewhere too, because he is responsible for the first IRC chat clue. Either that or it was sent before the onset of the BMRF massacre and he is now toast because of it.

Anyway, I've done the best I can to provide some sort of narrative, and even if it's completely wrong (which I'm sure a good chunk of it is), I hope it will still spark some fresh lines of thought.

Summary of Clues:
When we first discovered the codes, we noted that there were four codes to be found. These codes were set up by Dr. Horn, which led us to realize it was Stormseeker (Chris Horn) setting up the majority of this. The primary code D, the one that led to the last digits needed for the "thepizzaisalie" site, was directed to a Dr. Bottomley, who has since been identified as one of Storm's friends.

There were also a couple of IRC clues given prior to the solving of the other web-based clues. These were:

N38°57'8.05" W77°8'44.82". Solution two ignore loc data N32°52'50.77" W106°20'49.40" not buried at initial loc, fly here. Travel 14.16 miles east we transferred the niobium there. Await further instructions. And broken into pieces:
 * 1) The IRC clue "editing" the Konami Code cipher (Code A), although it has been hinted that the original form "bon ami" was intentional, for it means "good friend".  This chat clue also states, "Don't let him find us--Dr. Welsh", suggesting that Dr. Welsh was a key player in the ARG, as well.  We found out later, via Welsh's profile site, that this is the case.
 * 2) The second IRC clue that first mentions coordinates:

38° 57' 8.05 N 77° 8' 44.82" W The Kryptos Statue in CIA Headquarters, Washington

32° 52' 50.77 N 106° 20' 49.40" W White Sands Missile Range, New Mexico

-15' 49.35" W 14.16 miles East of the first location leads to a Domino's Pizza in Washington

-14' 39.84" W 14.16 miles East of the second locationleads to a fairly deserted looking area close to Hollomans Air Force Base mentioned inIRC clue 3.

3. The second location clue: INCOMING TRANSMISSION - LOC 2 LAYER 2 SUBSTRATA 3 X01/X02 HALOS PROJECT INITIATED 41Nb recovered. HAFB Compromised. Transfer to site complete, project HALOS underway. Further INFO [Classified]. CODE BASE 64 compromised, switch to old code talker. They are watching, assume leaker on site. WSMR No longer viable location, move to main site, check external sources.

Now, we have no idea who these messages are being sent to, but we can speculate that they originate with Dr. Horn because they mention the missing / hidden X01 and X02 rooms. They also mention the HALOS project which has become synonymous with Dr. Horn's later clues.

After discovering the website and solving the binary puzzle, we then began getting web-based puzzles. These began with this puzzle, that turned out to be Base 64 with a Navajo message inside of it, which then needed a Playfair cipher to finish it off: Proxyhost@-84-9-123-164.dslgb.com//closed.proxy.accepted//?OTR,1,3,?OTR:[I---MI-G TR --SMI---ON - UN---WN S##RCE] Access detected to personal site. Security compromised. HALOS project under threat. Site offline as response. Switching to new protocols. [********] ~[OTR//2.0]  

Solved portion: primesitecompromisedreturnbmrfloginhalos   After solving this, we received another clue in chat, also in Base64 that used a one-time pad encryption. Brute-forcing it using key words eventually led to it being solved: [[Proxyhost@-84-9-123-155.dslgb.com//closed.proxy.accepted//?OTR,1,3,?OTR: [INCOMING TRANSMISSION UNKNOWN SOURCE]LEAK SOURCE DETECTED. TRIANGULATING...MIX CASCADE HOP DETECTED...ATTEMPTING TIMING ATTACK...[TERMINATED] CANNOT CONNECT TO HOST... ATTEMPTING CONNECT TO USER H... SENDING DATA. SECURITY LEVEL 7 ALPHA.  [OTR//3.0]

Solved portion:

"This is a message left for Dr. Horn. Just to remind you in case of  emergencies that the password to the HALOS files is BENALOHPAILLIER. I have programmed HALOS to send in level seven cases. You should bring  pizzas."  We now see that we have a login for the HALOS project, as well as a password. Furthermore, there is someone else sending these messages because they are being sent to Dr. Horn. Could it be Welsh? Bottomley? Or a new entity altogether?

Lastly, we received a new file on the "thepizzaisalie" site--this HALOS.txt file is the one we're stuck on now, and the message is thus: [[Proxyhost@-84-9-123-345.dslgb.com//closed.proxy.accepted//?OTR,3,4,?OTR:[INCOMING TRANSMISSION CLASSIFIED SOURCE]SUBJECT ANALYSIS - TENACIOUS. SITE OFFLINE......'...{Primary Servers Overloaded}... USER ACTIVATION REQUIRED... PASSCODE INPUT FOR SITE ACTIVATION REQUIRED...'SET FOR FINAL TEST PATTERN....'ANALYSIS COMPLETE>>> [CLASSIFIED INFORMATION LEVEL 8][OTR//4.0]  B32B003A 35BADD66 577C24C1 4FC91906 4346D131 A7C54BB8 2FFE03E0 22615777 247923DC 21F62CD4 182E91C3 B267B545 ABCAEDAF 0261510D 4EEA1E87 CD33C7C7 7131309C C4280EB4 243D1154 F044F9CF 6296D9BF F7397E43 90987FE6 3203DA0D E40278B3 A54F5DDC 6975FA04 F749849E 1A62595A 9F630B07 95913DE0 153E3AAC 388C45FB 9D850CFE 913541D6 C08398F2 C88332A8 2FDF0028 1D62FCDC 4FE7E46A E90C51C5 C806B411 64E33AB9 2C96862E 068B0C16 C09990B8 381A00DA 7915B67F E4A20F59 9B0F1B6D 481913C7 B9538CEE 639144F4 1561BA92 E4FE751D 1E242CD8 8F51D695 51988713 6A7C15AA BD7B4004 49220141 30A91F17 0F66CCB3 C139463A 7E909A37 AA863FB2 7805FC97 31C09C8C 79067E79 930A4065 46B24C9A 629B26C2 CE2A4BE4 8F589A37 5FEB731F C4AB225C 11848CF8 9E291FB2 7133970C 06361847 4A892801 EDD68F54 698C5E5B 506746F6 765A6F7F 1225DEA4 DA1140FE B60F6507 45241C69 3695883D CB21E6FB FEFBB85A 29919480 36A52B5D

[/][End Transmission]|¬[ABORTIVE.] [Transmission Ends]] 

We may be stuck here, but I think we have all the information we need. We have a login and a password, and I don't think the password is a direct key to the actual cipher, but should simply be used to access the HALOS site, whatever that may be. We seem to have overlooked the other clues, and I think we need to put them together to make this next big leap and pass through the gate to the next portion. With this in mind, maybe we need to look at other possible sites / links that have previously been added or left undiscovered.