Proven through a screenshot from the Gameplay Premiere, SIVA returns in Destiny 2. The only crucial thing we did in Rise of Iron was destroy the Replicator. Not even killing Aksis did all that much to end its threat.
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Somewhere in the grimoir it mentions there is a ship that left Earth that was filled with SIVA. Think Mylan touched on it in one of his videos a while back. I was hoping not to see it for a while, but oh well.