As per the Halo device on page 100 of the Disciples of the Dark Gods book.

Phase one is pretty simple. (Gain, Unnatural Agility (x2) and Unnatural Toughness (x2))
The problem lies with phase two.

The character: Gains Unnatural Agility (x3), Unnatural Strength (x2), and Unnatural Toughness (x2).

Now does that mean, since Unnatural Agility is already at x2 from phase one, increasing it with the 2 additionals listed (x modifier -1) would bring it to Unnatural Agility (x4)? or would it just bring it to Unnatural Agility (x3)?. In which case it would be better written as: Increase the Unnatural Agility multiplier by x steps and if they did not already have this trait give them Unnatural Agility (x ..).

I don't mind either I would just like to know how hard my fallen tech-priest in power armor is going to be to kill by a) my minions, b) the rest of the party.

IIRC, the example character afflicted by a Halo device replaces their Traits with those relevant to the current phase. So a character would gain, i.e. become, Unnatural Agility (x3) in phase two rather than have the two Traits combine to become Unnatural Agility (x4).

While the device is certainly supposed to be powerful, the combined effect of all those Unnatural Characteristics if they were cumulative by phase three would be a bit excessive imho.