10 Deleted Scenes That Explain Confusing Star Trek Moments
2. Star Trek: Deep Space Nine - Why The Prophets Chose Sisko
The Mystery:
Why did the Prophets choose Commander Sisko to be their Emissary in DS9's "Emissary"?
The Deleted Scene:
One of the few actually useful deleted scenes from a television episode, this scene was intended for Star Trek: Deep Space Nine's pilot episode but cut for time.
In it, Sisko would have returned to Bajor to meet with Kai Opaka after his experiences with the wormhole aliens aka the Prophets. Opaka would've explained to Sisko that the Prophets chose a non-believer and a human to be their Emissary because "one should never look into the eyes of one's own gods".
The line would go on to be repurposed in the season finale, "In the Hands of the Prophets", but it would've had much more impact if it had stayed in the pilot. It's the perfect encapsulation of Sisko's relationship with the Prophets and while the show went on to expand on that dynamic, nothing is as concise or reasonable as this deleted explanation would've been.