Well after reading Sonic the Hedgehog 195,Sonic Unverse 1, 21-24, and Eggman Nega's page in the Complete Sonic Comic Encyclopedia. I a huge idea on his backstory. Well it kinda involves the games since in the games Eggman Nega comes from Silver's time and travels to Blaze's Dimension(revealed in the story of Mario and Sonic at the London 2012 Olympic Games for 3DS). I had a story idea and I would like to share it.
It all begins in 3257 Eggman is fleeing from older Sonic and Knuckles. He goes to the remains of his base and puts himself in stasis so he can return when Sonic and Knuckles are elderly. But Sonic sets it to 3427 instead of 3297. When Eggman awakes, he is shocked by the year. He then decides to change his suit and adds Nega to his name so he can disguise himself from the Mobians that might reconize him,(He fears because they might know him from History Books)but when he leaves the remains of his base.... He finds that Mobius is different. There are tiny villages all around the world barely holding any Mobians. In the remains of Central City he finds Mammoth Mogul and a four year old Silver the Hedgehog. That then begins the feuds between Silver, Mammoth Mogul,and Edmund with Eggman Nega. Eggman Nega attacks Silver with schemes simular to his attacks at Sonic. But to try to kill Silver, Mogul, and Edmund he releases the Krudzu Spore. It kills almost a third of Mobius' remaining population. Silver manages to defeat it and send Eggman Nega packing. In the early spring of 3437 P.X.E, Silver the Hedgehog is training with Edmund when their archenemy Eggman Nega attacks Onyx Island. He has a robot named Metal Sonic. He says he traveled to 3237 in a "Sol Dimension" and found its remains in the ocean. He states that he upgraded it and wants to see who is the better Hedgehog. Silver fights the robot and defeats it.(This is how in Sonic the Hedgehog 195, Silver reconizes the Metal Sonic model. In fact it is the same model). Eggman Nega leaves to the Sol Dimension. And thats how the story all begins.