What causes the check engine light to come on and the engine miss fire?

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When battery weakens usually due to little use, the brain causes all kinds of electronic malfunction. Fuel low and gauge says empty but I have 3/4 tank of fuel. Codes show miss fire and transmission stops shifting. Reset used to clear all once batteries where good but now it wont. Is brain or components of it gone bad? Codes are P0202, P0203, P0205, P0208, P1262, 2 INC Misfire, Comp, 1 ready. It's just wierd.