My prediction (albeit a bit far-fetched) is that the intern will actually frame Dexter for his (the intern's) set of serial killings. Masuka said he'll keep throwing him some work as a consultant which means that he can tamper with/plant evidence framing Dex. I think it would be interesting to see Dexter get framed for murders he did not do, especially since Deb has now seen him murder somebody so she'll have no idea what to believe.
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