He did that by being a conniving individual that tricked the party more than once.
In Ginaron he assumed the role of Temple 1 and guided the characters through that facility till he found the Controller there. He then used a strange U-shaped tool to assume control of the Controller. Despite Little One's attempt to grab him, he managed to be able to achieve his goal into letting the portal achieve critical mass so it would saturate the surroundings in astral energy, infecting every living thing in a huge radius with the Astral Plague. Thankfully the players could diminish this plan.
After that he sicked his friends to harass the party, with Delta probably sending some orcs the Party's way and Beta and later Delta even fighting the Party directly.
The next more or less direct confrontation was at the entrance to Polaron where Epsilon send the aberration of a Dark Ancient Gamma against the Party.
After several more harassment in Polaron Epsilon confronted the Party in the great Portal Room inside the body of the Strategic Withdrawal Unit and finally died.
Epsilon may have been the "Leader" of the Dark Ancients insofar that they accepted some of his suggestions like having a large number of Warforged put in suspended animation so they could posess them at a later time.