Sonnie's mind was put into the monster... she became the monster after the attack.
The "human" body was actually a cyborg remotely connected to the monster through a neural link, which is why it kept talking even after its body (and brain) became a gory, lipstick-stained puddle of mush.
As for Aquila Rift... the slipspace portal would send ships out into deep space -- or through some parts of space that humans should never travel to -- and as others mentioned, there were extradimensional or other-worldly creatures that would capture ships in an organic web and feed on the inhabitants until they died. Not all the ships that passed through the portal went there but some did, usually when a temporal anomaly would occur.
Part of the dangers of deep space travel is that there are things beyond the comprehension of man, and Aquila Rift dabbled in the concept of a sector of space where Lovecraftian horrors roamed free between destinations deemed "safe".
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