User blog comment:DeadDATA/Cerberus In ME3: How They've Grown/@comment-2256917-20110822014820/@comment-3566082-20110822034923

Cerberus aligns itself with the Reapers by time ME3 starts. They probably arent worried about dealing with the Reapers anymore. They were probably tasked by the Reapers to kill Shepard specifically. We all remember the interest Harbinger had in him/her during ME2.