Covert Infiltration
This is an interesting one. Essentially, agents that have been surgically altered to resemble individuals from a primitive species are sent to infiltrate their society. Political and military leaders are gradually replaced, until a point is reached where the primitives can be made to willingly accept an offer of annexation. This spares the need of a messy ground invasion, but more importantly, the primitives will be more positively inclined towards their new overlords, since they are living under the illusion that they accepted their rule willingly.