At the end of the Mission Attican Traverse: Krogan Team, you’ll have a choice whether to spare or kill the Rachni Leader.
Choice: Spare the Rachni Leader or Kill the Rachni Leader
This choice can change a fair bit depending on your choice in Mass Effect 2 regarding the fate of the Rachni Queen, if you saved her, she’ll be present in this mission, if you killed her, she’ll be replaced by the Rachni Breeder. The choices below will be split between the Queen and the Breeder for easier reading.
Choice: Rachni Queen - Help her escape
With the Rachni Queen present, If you choose the option “Help her escape”, you’ll gain the Rachni forces as a War Asset and gain a massive 100 Military Strength.
Choice: Rachni Queen - Leave her to die
With the Rachni Queen present, if you choose to “Leave her to die”, she’ll accept death gracefully, but you’ll lose the Rachni forces as a War Asset, gaining the Aralak Company in its stead, however, you’ll only gain 25 Military Strength.
Choice Rachni Breeder - Help her survive
If the Rachni Queen died in Mass Effect 2, the Rachni Breeder will be her replacement, by choosing to “Help her survive” she’ll become indoctrinated a few missions later, and wipe out both your Aralak Company, and Rachni forces Military Strength as well as a large portion of the Alliance Engineering Corps.
Choice Rachni Breeder - Leave her
If the Rachni Queen died in Mass Effect 2, the Rachni Breeder will be her replacement, by choosing to “Leave Her”, her children will kill her, keeping the Aralak Company forces intact, and still part of your Military Strength.