Leto II is a Worm.

He is within the ever present now.

Nyla was ordered to do whatever Siona wanted, even if it was detrimental.

Leto II foresaw his own demise at the hands of his one and only love…this is why Leto II gave Nyla the order.

Siona wanted to assassinate Leto II, and knew his weakness.

His Worm manifestation was vulnerable from water from evolving in the desert, so as Leto II was crossing over a bridge that spanned over a river, Siona commanded Nyla to take the bridge out using a Lasgun.