Take into consideration this is based on a series of Light Novels. And every novel has its own story.

For instance... episodes 1 to 5 where the first novel. 6 to 9 are the second novel. Episode 10 began the 3rd one, which features the second co-heroine mostly.

Despite the series having the name 'Index', the main character is Touma, and the two co-heroines are Index and Mikoto. It just happens that Mikoto didn't have really much to do, sans the 'prologue' (first episode)

Mikoto became so popular she got her own manga in the 'A Certain Scientific Railgun' series, where Kuroko is the co-star. Touma appears as well, but Index doesn't.