Champions Online/WMG

The entire contents of the game's story is the result of one or more Big Bads puppeteering EVERYTHING..
Why: Because the actual heroic Champions, the canon guys... They're pretty ineffectual. Kinetik, the speedster, barely moves... The other heroes are split up across various parts of the world... And Defender... He can't deal with 10 low powered robots and a door without your help in the tutorial. So, perhaps they've each been weakened or perhaps manouvered through some major Puppetmastering into being each incredibly weak, whilst attempting to train You into becoming a worthy adversary by stimulating conflicts everywhere. [this post needs a bit of Wiki Magic, as I've no idea how to edit bits to look like other WMG pages]
 * Unlikely. They are much more competent in the new tutorial.

Kevin Poe will be the Big Bad of a future zone.
Recently Kevin Poe and Wayland Talos had their powersets changed. Talos' is appropriate, now that he is wearing a power armor. Kevin Poe, however, had his force powerset changed to darkness and munitions, the former of which seems really out of place for anyone familiar with his character. My theory? Cryptic got plans for him, and this change is actually foreshadowing that Kevin Poe will be important in the future. My theory is that Kevin Poe will be the Big Bad of the upcoming zone, having taken a level in badass. In addition the rest of the Westside gangs will make a comeback as Kevin Poe's underlings and lieutenants, stronger than ever.

Mr Gemeni is never actually defeated at the end of his missions.
Which is why the Gemeni gang doesn't go away after you send him to jail.