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It kinda acts as a bridge between DX:HR (which is set in 2027) and DX 1 (which is set in 2052).

Morpheus is an AI (which is what Bob is referring to when he says the Morpheus Initiative) who features in Deus Ex 1. As for the nanite-virus that Megan mentioned, that's the Grey Death which plays an incredibly important part in DE. If you play through DE1 again (assuming you have, if you haven't then you really need to play it) you'll make the connections between them.

At least, that's what I'm gathering.

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