Any story can have a good protagonist, but the only way to make them great is to face them with a greater antagonist. The Halo franchise serves as the perfect example of this, with the Master Chief and 343 Guilty Spark, respectively. While it might be easy to say that the main antagonist in the series is the Covenant or perhaps the Flood, Guilty Spark serves as the perfect foil for Master Chief in ways that none of the other villains in the series can.

Source: N4G PC 343 Guilty Spark Was Halo's Best Antagonist