This theme first came up in Baxter's short story “Sheena 5”; see Variety SF for a review, which is much more about the squid and less about the humans.
A squid will have her mind genetically enhanced to make her smart, & to make her communicate with humans [...] she got pregnant just before the trip. Since she is smart, she gave birth in space in a way that hid the fact from mission control for too long. Now her craft is on asteroid, the rocket is fitted to asteroid & pushing it towards earth, but she has too many babies in her too small a habitat!
Turns out 4 of her babies are very smart; rest are typical dumb squids. Dumber ones will get eaten by their smarter siblings. But soon, the life support starts getting overstretched. [...] Not only have the squids made their little asteroid wholly habited, they have ships all over Sol! Reinmuth is headed to earth, & humans are afraid. Near end, we will see hints of the doom of humanity - as nuclear attack against Reinmuth fails, & it's entering earth's atmosphere. Sheena 46 appears to be in charge.
A squid is genetically modified to be intelligent enough to pilot and land a spacecraft; she manages to proudly complete her mission without letting her ground controllers know that she managed to get pregnant on Earth. A few of her offspring inherited her intelligence, and the end result is a whole colony of intelligent squid in space.
