What role do the Covenant play in the Reclaimerverse?
The Covenant do still exist, but in the Reclaimerverse, they currently have an uneasy truce with humanity. First contact was still made at Harvest, which was still glassed, as were a number of other human worlds. The difference here is that the Flood is much more numerous and more insidious than they are at first contact in the Haloverse. The level of threat they pose to humanity and the Covenant alike is so great that the Covenant were forced to put aside their campaign against humanity – though perhaps only temporarily – in order to join forces and fight back the infection before it can totally annihilate all other life.
