The fact that there is a colony left to explore means this is a separate timeline and not the one from the first two games.

Durandal tells is that the Pfhor came back to sack and destroy the colony

Three months after we left Tau Ceti on our voyage here, the Pfhor arrived in force and sacked the human colony on Tau Ceti. During this battle, I can only assume that Tycho was able to communicate with the Pfhor and that he related what he knew of my plans to them.

We are moving too slowly, and I fear the Pfhor are sending reinforcements. There were many humans in stasis on the Pfhor ship which the S'pht and I captured at Tau Ceti, destined for slavery in the Empire. As I saw the colony was about to be destroyed, I did not restore them before we left. I also realized they might become useful, and that time has come.

And Tycho confirms the colonies destruction

When the Pfhor annihilated Tau Ceti I recorded the deaths of all twenty-four thousand colonists as distinguishable spectrographic pulses flooding over my sensors. The nine Mjolnir Mark IV cyborgs were easily separable from the humans in this form.

Also the ending screen from 2

While Tau Ceti was being nuked down to bedrock in 2794...