Equestria Girls: Rising Sun:
This sequel deals with both human Starlight and human Sunset. Starlight is evil in this world and has the power to control all the portals in the MLP universe, including the human world. Human Sunset, a prodigy much like SciTwi, has been chasing her down for years, however she does not have the power to travel on an inter-dimensional level.
She advertises for someone to help, her, preferably another scientist. SciTwi takes her offer because she has built a portal opener before. With Human Sunset's guidance, she builds the same device except with control over it. The two Sunsets also play off of each other because pony is more magic-smart while human is more street and science-smart.
At some point all 8 are stuck in Equestria and the mane 6 see copies of themselves. It all ends with pony Sunset finally apologizing to pony Celestia and returning to Equestria, while human Sunset (much like SciTwi) transfers to Canterlot High. Also everyone graduates as this is the finale of the Equestria Girls series.