Jun is dead. If you've read the book Halo: The fall of Reach (Which I doubt) it states that Dr. Halsey's escort (Jun) died protecting her.
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Your bump has reminded me of 343i's stupidity. Why?
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That Adjunct short story was referring to the SPARTAN-II who died protecting her, before the cryopod she was in was taken. Essentially, a lead in to the Halo Legends episode "The Package". Jun is indeed alive and well.
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Don't I feel stupid lol.