Not that I have any special knowledge of what the devs' plans are, but I must imagine that the episode missions will return at certain intervals (assuming the game's successful and doesn't fall apart). For example, while the TV show's on hiatus and there are no new episodes, I could easily see the "older" missions coming back for a short time.
While Star Trek Online doesn't remove the old "featured episodes," it does cycle through them and give new rewards. I think Defiance will do the same thing eventually.
i imagine they will put all the episode missions back after the first season of the show is done
Because they will take this missions off
The current Episode missions are a prequel to Episode 1 of the TV Show. So if you watch the first Episode before playing the first Episode missions, you'll spoil the first Episode missions for yourself!
I don't think they're going to be removing these missions, but for the best experience they expect you to play the current episode missions now. Then play the next Episode missions before the second Episode of the TV Show, and the next before the next, etc, etc.
"My opinion is, my opinion, is my opinion."
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Its a fairly good bet they will infact remove them, infact they have implied it on several occasions.
Having them in game while the show is ongoing would be immersion breaking, and there is nothing in these missions that you need to play the game.
However I could see them coming back off-season even though I don't personally support that.
They are structuring the mission releases like a tv show season does.
Obviously there are going to be re-runs
and eventually Syndication,
Followed by the Blu-Ray/DVD Box Set.