Episode quests don't work

Not trying to be a smart a** but are you sure you are upgrading and not slicing?

What is the difference? I go to my characters and the mod view and wherever I see a mod with a dot, I click on it and if I have enough mod amplifiers, I up it to the next level. As well, when it gets to the top level I do that thing where I spend 15 micro attenuators to see if a stat will change.

You’re slicing, not upgrading. Level 1-15 is upgrading.