uh...no....end of the third game the covenant got fucked over...there the only implication of "an ancient evil that threatens all the universe" would be the flood...but they got wiped out as well....so whats left?
The Flood will not appear in Halo 4 The Covenant will appear again but without the Prophets at the head; perhaps led by the members of the "Servants of Abiding Truth" (Halo: Glasslands)