Linkin Park/WMG

Most of the songs on Linkin Park's first 2 studio albums are the halves of a person with split personality disorder arguing with each other.
It applies to most of the songs - they're all ranting at an unspecified "you", and most of them feature lyrics including internal pain and self-harm. It doesn't work for all of them, but the ones with a clear rapping/singing dichotomy often seem to be addressing and ranting at each other. Even songs without this structure makes allusions to it sometimes ("Against my will I stand beside my own reflection" in Crawling, and basically all of Don't Stay). Figure.09 seems to be the flashback "Origin Story" of this disorder in the unnamed protagonist... and then "Numb", the final song to the 2nd album, is him finally overcoming the disorder and ridding himself of the "voice in the back of [his] head".

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That sort of makes sense.

The members of Linkin Park think they've been chosen to save the future of mankind.
Linkin Park's first 3 full albums were full of songs mostly centered on Chester's scarring past and teenage issues like being yourself and not fitting in. However, in A Thousand Suns, Linkin Park COMPLETELY changed their sound and the messages they were sending. All the songs were about nuclear war destroying everything. Part of "The Catalyst" even has the band yelling "GOD SAVE US, EVERYONE" It's possible that Shinoda had a revelation from God that we are going to destroy ourselves with senseless war, and that the band has to do something about it. Unfortunately, the only thing Linkin Park can do is make an album about it... but it's more than an album. It's a flat-out warning.
 * That doesn't explain Minutes To Midnight. They had a new sound and a few protest numbers on that album even before A Thousand Suns.
 * Minutes To Midnight did have a few protest numbers, but the whole album wasn't dedicated to war. Most of the songs were just about random subjects, such as "Valentine's Day" being about losing your lover and "Bleed It Out" being about the pain and misery in trying to write good songs.

The mysterious virus in the Australian version of the "What I've Done" music video is the T-Virus of Resident Evil fame.
The pharmaceutical company that created the virus looks suspiciously similar to that of the Umbrella Corporation, and the description of what the virus was supposed to do ("social control") certainly fits the destructive nature of the Ebola virus, from which the T-Virus spawned.
 * Wasn't the T-Virus reverse-engineered from the Mother virus, which was itself found in a dead queen ant?

"Bleed it Out" is a Stealth Parody of their first two albums.
Let's briefly analyze the lyrics. The opening line pretty much states that we've heard this before, highlighting their oft-used formula. There's a reference to "In the End" with the lyric "Doesn't matter how hard I try". Finally, then there's the line "Half the words don't mean a thing and I know that I won't be satisfied" which seems to call attention to their past wangsting.

Mike Shinoda and Chester Bennington were switching roles in "Blackout"
It's very possible this wasn't an intentional design, but still, think about it: Chester is more or less rapping for the first half of the song, and later Mike joins in with soft singing vocals.

"She Couldn't" wasn't kept out of circulation because of the High and Mighty sample.
It was done to sell the band as pure nu-metal. Their songs from 1999 fell into two categories: angsty nu-metal and cocky alternative rap. On Hybrid Theory however, the only overtly hip-hop track was "Cure for the Itch", which didn't amount to much more than a short interlude. Everything else on that disc was the introspective and easily marketable sound they became famous for.

There is some strange Linkin Park/Pokemon conspiracy going on.
Put another way, the nth Linkin Park major album release is always released within 30 days of the n+1th Pokemon RPG generation debut. Linkin Park is an American band, so the American Pokemon release dates (except for the last) count.
 * Hybrid Theory, Gold/Silver - October 2000
 * Meteora, Ruby/Sapphire - March 2003
 * Minutes To Midnight, Diamond/Pearl - Mid May/Late April 2007
 * A Thousand Suns, (Japanese) Black/White - September 2010
 * Living Things - June 26, 2012; Black/White 2 - June 23, 2012 (Japan)

To boot, The ATS CD and DVD covers follow the same coloring and design scheme of the Black and White covers. Something is clearly afoot.