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A rainbow is an optical and meteorological phenomenon that causes a spectrum of light to appear in the sky. Rainbows are also an international symbol of homosexuality and LGBT rights. Unfortunately, Chris didn't know this when he wrote them into the comic, leading to hilarious results.
For Chris, a rainbow is both an important part of the plot of the Sonichu comic and a lazy metaphor to represent something happy, amazing or pleasant. Rainbows played an important role in the history of the Chaotic Combo. Trolls got good payoff by exploiting both Chris's naivete and his intense fear of becoming a homo.
Several years later, Chris became a lesbian transgender, and to his relief was able to unapologetically bring the rainbow back into his life.
Chris and Rainbows
Chris has a long history of incorporating rainbows into his artwork. A few of his homemade Pokémon cards are rainbow themed, such as Snowboarding Sonichu, Supreon and Turbo Rainbow. His Pokémon Vegaton is described as being capable of creating rainbows. In 2005 he created a rainbow star featuring himself and Sonichu for the top of his Christmas tree. He has admired the fact that his high school ring includes an image of a rainbow.
However, in addition to not knowing that rainbows are used by "da homos", Chris has utterly failed when trying to replicate them. Apparently, Chris was never taught the simple concept of ROY G BIV, which gives the exact order of colors in the light spectrum from left to right. As such, Chris repeatedly mixed up the colors of the rainbow. This demonstrates two things: firstly, that Chris was too lazy to find a reference of a real rainbow when drawing the comic; and secondly, that Chris knows nothing about how rainbows are formed.
Like GodJesus, Chris sometimes offers people "rainbows of promise" as a half-assed apology for things he has done wrong. For example, he offered Megan Schroeder a "rainbow of promise" while corresponding with her after the shecameforCWC.JPG incident. Thankfully, Megan saw right through his shitty apology and cut him out of her life. In another example, following fan backlash against the hardcore sex scene depicted in Sonichu #8, Chris removed or censored the pages containing genitalia from the site, and issued a "rainbow of promise" to not post any more sexual imagery. Chris drew love scenes between Black Sonichu and Silvana Rosechu in the very next issue. These serve as examples of not only his insincerity, but also his disturbing insinuation that he is divine.
In the Comic
A rainbow effect is created when Pikachu strikes Sonic in Sonichu #0. This energy also arcs across the sky, striking a female Raichu some fifteen miles away, and transforming her into a hideous hag beast. The irony of Chris's most prized creation coming from a rainbow, a long-time symbol of homosexuality, was lost on him.
In Sonichu #3, Chris revealed that the Rainbow had also spit out five eggs which landed in various locations around the world. Hence, the Chaotic Combo. Chris should be feeling pretty gay right about now. Sonichu would soon discover other Sonichus and Rosechus which were created by the Rainbow. So basically, most of the Sonichu characters came from a rainbow. The various Sonichus and Rosechus represent every color of the rainbow, although this may be a coincidence, as there's so damn many of them that Chris has no choice but to use every possible color to tell them apart.
In addition to the eggs, Chris established that "mysterious beams of light also shone from the rainbow", but declined to elaborate; this might be Chris's way of giving himself an out for adding more Sonichus and Rosechus, like Silvana.
Trolling and comic retcons
Given that one of the trolls' favorite games was calling Chris gay, it was only a matter of time before they would use the rainbows as ammunition. Jimmy Hill, a troll-illionaire who managed to make billions of dollars from the Sonichu franchise by turning the main character into an LGBT icon in late 2008, made a point of incorporating rainbow imagery into his original creations. Even worse, in January 2009, Chris learned that the internet forum Gay 4 Sonichu was using his comic to promote homosexual deviance. He exploded in outrage at their appropriation of the rainbow. "I do not understand why the f*** the gays decided to use Rainbows as their symbol; that's like asking Hitler why he used the Swastika (which originally was a Lucky Symbol) for his whole mess."
Thus, reluctantly, Chris went on a campaign to remove and/or alter all homosexual symbology, including rainbows. Most notably, the infamous "Rainbow Chris" image from Sub-Episode 2 was changed to a background of the gates of Heaven, which implies an arguably worse outcome.
The rainbow returns
For a long time, Chris sulked about the homos' misappropriation of one of his favorite symbols. Then, in August 2014, he suddenly realized that he himself was a member of the L(g)BT community. He announced this to his Facebook family by posting a picture of himself holding a rainbow flag. Since then, he has been unashamed to festoon himself with rainbows and all manner of girly imagery, especially that related to My Little Pony and the Equestria Girls spin-off. However, given his hopeless confusion about gender and his hypocritical hatred of the homos, it's anyone's guess how long this rainbow renaissance will last.