From the beginning of the Earth, and at every individual age of civilized beings, there has been a protector of the Earth who, from birth, was granted the power to protect it and its inhabitants from harm. There usually will only be one, as only one is needed; however, certain circumstances allow for more than one to exist at once, such in the case of Shadow, and Chaos. This character would be born not only with great power, but with a .heroic and noble character. Sonic would be one of those great and noble protectors who inherited this noble character to stop evil from overtaking and destroying the Earth. This would explain why Sonic is always to eager to help those in need and save the day from Doctor Eggman. The Chaos Emeralds, which could be have had the original name of Emeralds of the protector, as well as the master emerald which governs the other seven, could be have been created for use of the protector, as there may be times his powers aren't good enough, and he needs more strength to protect the Earth and save the day. Simple concept, but it would add depth to the Sonic Universe.
Shadow would have originally been the protector of the Earth, as he inherited it's power at birth, but his hedgehog village is attacked by a savage neighboring village who kills everyone, except the village priestess and her husband (Possibly Shadow's parents are the ancestors to Sonic, and are about to kill Shadow when, due to the extreme emotional distress he's undergoing from seeing his so many of his people die and as well as being in danger of dying, his guardian powers that were yet to be unleashed were then released and he not only destroys the all of the attackers, but the whole surrounding area. After rampaging, Shadow collapses and passes out exhausted. The havoc he caused permanently altered the landscape creating the Pumpkin hill type area.
Shadow startled, confused, awakes in the Space Colony ARK. Professor Gerald was on a "research trip" to find another specimen for his ultimate life project for the government, project Shadow but is truly seeking for plants and animals to cure the disease his granddaughter Maria had, found Shadow and nursed him back to health. Shadow, who was near death, recovers almost over night with an accelerated healing ability granted to him by being the guardian of the Earth. This gives Gerald the idea to use Shadow to make a cure for Maria. Gerald moved him to the ark with power inhibitor rings placed on his wrists to restrain his destructive power. He also invents a teleporter that connects from the A.R.K. to his secret pyramid base, he keeps from the government, in case he needs to quickly escape the A.R.K.
Gerald's granddaughter Maria, who is his favorite because she has always taken an interest in her grandfathers' work and thus, earned her grandfather's trust, was raised on the ark and is a patient there after being Diagnosed with NIDS (Neuro Immune Defiency Syndrome) at a young age. She does not remember what it's like to be on the Earth as implied in SA2. Dr. Robotnik hasn't told Maria about Shadow's rampage nor how potentially dangerous he can be because he secretly hopes her natural warmth and affection can help Shadow to control his powers. Upon seeing him, she gives Shadow his name due to his black furred appearance and inability to remember anything from his past. Maria spend a lot of time together and become very close. As Shadow has not had any problems controlling himself, Gerald plan seems to be working.
Before he found Shadow, Gerald was working with his fellow scientist, Professor Freud Sigmund, head of Project Biolizard, on creating the Ultimate life form. When Gerald found Shadow, he presented him to G.U.N and showed them pictures of the destruction Shadow had caused as well as before and after photos of Shadowing recovering. To prove Shadow is capable even further, he says, " Still not convinced? Let me give you a little demonstration." He then proceeds to remove Shadow's cufflink inhibitors and Shadow, then concentrates and moves his arms outward. As he does this the whole building begins to shake, and the G.U.N commander tells Gerald to stop him. After Shadow stops, G.U.N. appoints Gerald as head of "Project Shadow" and removes funding from Project Biolizard.
When GUN invades the ARK Maria manages to enter the capsule alongside Shadow. Maria, being an idealistic, tells Shadow how much the Earth and the people on it mean to her, asking him to promise to protect it which of course he does. As Maria and Shadow are hurling towards the earth in the capsule it begins to overheat and malfunction, in this desperation Shadow's powers kick in and he uses a chaos control to teleport them out of the capsule. They are teleported outside of prison Island where they are quickly apprehended by GUN. Shadow is encapsulated, and Maria, while no under arrest, stays at Prison Island to wait for her Grandfather. When he arrives she's allowed one visit with Gerald before he's imprisoned. They get to talk and Gerald secretly hands her the disk journal he made with the true record of what occurred, a video recording for Shadow, and one for her as well. He forbids her to present this to GUN because he doesn't want Sigmund to target her or alter it before his trial. After Maria describes the events to Gerald, and after seeing she no longer moves with crippled impairment, Gerald deduces that when "the bright flash of light (chaos control)" occured Shadow's cellular regeneration must have spread to her and cured her which it in reality did. By knowing this Gerald is overjoyed and no longer cares what happens to him as Maria's life is saved. The soldiers make her leave and she then goes on to live a long healthy life harboring the secrets of the day. She is still alive when Shadow emerges 50 years later, and meets him again eventually.
After Gerald is taken arrested by GUN Sigmund sneaks onto the ARK to frame Gerald when an investigation is done on the ARK. He programs it to crash in the earth, makes a false recording death threat of revenge by Gerald, altering parts of Gerald's journal, programming the ARK canon to destroy the Earth and look like Gerald face, and reprogramms the biolizard.
Upon investigation of the altered lab on the ARK, GUN finds Gerald guilty and sentences him to death.
Sigmund makes sure to alter Shadow's memories so that he couldn't testify in Geralds defense should they question him. Maria getting shot was an altered memory. Sigmund had been observing Gerald carefully ever since Shadow was brought aboard, so he knew that Shadow's mind was too strong to be directly altered. He witnessed the bond Shadow formed with Maria and knew that the best way to manipulate Shadow's was through his heart rather than his mind, so he used his attachment to Maria to deceive him into believing he wanted revenge.
The events of SA2 occur with the alterations made her being added in, and now after sonic adventure 2. Shadow uses the majority of the energy from the chaos emerald that turn him and sonic super, to teleport to Sonic back onto the Ark, since he knows he has more reasons to live as Shadow believes he's just an experiment and nothing more; however, there was still some energy left, and this allowed him to use chaos control to slow the fall of the space craft. He was in thinking of Maria while doing such.
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