During the events on Noveria you’ll have to determine the fate of the revived Rachni Queen.
Choice: Kill or Spare the Rachni Queen
Defeat Matriarch Benezia and you’ll have to make a call regarding the fruits of her labors - what to do about the viscous, pestilential, galaxy-threatening monstrosity Benezia reared? No, not Liara - the Rachni Queen. The critter will make excuses for why her children were so hostile, but she’ll also make the mistake of reanimating the corpse of an Asari to use as her diplomatic proxy. Not a good look.
The Rachni Queen insists she intends to foster peaceful coexistence, but it’s worth remembering the threat the Rachni posed when they were free in the distant past. This time, the Council doesn’t have an unlimited supply of Krogan to throw at the Rachni. You can either kill or spare (and free) the Rachni Queen.
This one’s a bit of a downer. If you were worried about containing the Rachni, you can safely ignore that - they’ll be around in later games no matter what you do here.
Regardless of whether you spared or killed the Rachni Queen, you’ll be reminded of your deeds in Mass Effect 2, albeit fairly inconsequentially. If you killed the Rachni Queen, you’ll overhear a news report mentioning it. If you spared her, the Rachni Queen will send an asari thrall to thank you on Illium, promising - albeit cryptically - aid in the future.
Only in Mass Effect 3 does your decision truly bear fruit. Whether you killed or spared the Rachni Queen you’ll have to deal with a Rachni hive, although in the former case the new Rachni Queen is a clone, and in the latter case it’s the very same specimen you freed on Noveria. If you’re dealing with the genuine Rachni Queen, you can spare her again and she’ll faithfully serve you, becoming a War Asset. If it’s the clone… well, let’s just say the clone’s loyalty leaves something to be desired.