Okay so, this is only one of my many theories but it's also my favourite. Eddie Thawne is actually Hunter Zolomon, or he will be at least. Now, this comes from many clues my mind has drawn in. First, 'Eddie Thawne' is too familiar to Eobard to be a coincidence and I know we've found out that Eobard is a 'distant' relative of Eddie but I don't think that's the whole truth. Two, we've seen Eddie get more of a personality and more of a villainous? mind over this first season. Now, I know what you're thinking, bit far fetched right? Let me tell you the rest, I'll also be referring to the comics here so please beware of spoilers.
Hunter Zolomon was a transfer to Keystone City, Eddie was a transfer to Central City. Hunter and Eddie are both detectives.
After arriving at Keystone, Hunter became in contact with the flash and helped him solve many cases. Eddie has just found out The Flash's identity and has now been helping him and Joe.
In the comics, Hunter is in an altercation with Gorilla Grodd and is paralysed from the waist down and seeks The Flash's help! If you are unfamiliar with this, I'll make you aware.
"Hunter was severely injured in an attack by Gorilla Grodd in Iron Heights. The injuries left Hunter paralyzed from the waist down. He asked Wally West to use the time-traveling Cosmic Treadmill in the Flash Museum to prevent this from occurring. West refused, saying that he could not risk damaging the timestream. Zolomon then broke into the museum and attempted to use the treadmill himself. The resulting explosion destroyed the museum and shifted Hunter's connection to time. He could now alter his personal timeframe, giving the effect of super-speed."
Now, we have seen the Cosmic Treadmill in action but not to its full potential with the one based in Star Labs and we've met Gorilla Grodd. If you've seen the trailer that shows what's coming in the rest of the season, you'll see Joe in the sewers with Gorilla Grodd alone, but is he really alone? If this series has shown us anything about Eddie Thawne, it's that he will not allow Joe to go anywhere on his own. If Eddie follows him, could he be injured? Could Grodd get the best of him? I guess that's something we'll have to find out!
Let me know what you guys think!