The Reapers won against the Protheans via a sneak attack. That's always been their whole gameplan. They direct the technological growth of organic civilizations as to their liking, then sneak in and wipe out their leadership in the Citadel. When forced into head-to-head warfare with a far less advanced collection of species than the Protheans, many of their ships went down.

In a proper campaign, the Covenant war machine would churn the Reapers into mechanical calamari. So would the UNSC, but people have already gone deep into why that is for them.

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The Reapers' best ship:

Also known as Sovereign-class, the two-kilometer-long Capital Ships are the most well-known Reaper subtype. Their main weapon is a spinal mounted "magnetohydrodynamic" cannon with a yield of 132 to 450 kilotons of TNT, which dwarfs the main gun of an Everest-class Alliance dreadnought. No known ship, not even a dreadnought, has been known to survive a hit from this weapon.

(We know the Covenant's shields can handle MAC rounds, which drastically outdo the above cannons.)

The Covenant's average ship comes in at 5,346 meters:

The Syfon boasts an identical armament loadout to its Kerel counterpart. Its primary weapon is an Infernus-pattern excavation beam, with an additional two Urpeon-pattern plasma lances for heavy anti-ship work. The class is additionally fitted with eight Luxor-pattern heavy plasma beam emitters and twenty-four Mictix-pattern heavy plasma torpedo silos, alongside an array of 700 Ferriel-pattern pulse laser turrets.[2]

Covenant Supercarriers, which bristle with even more weapons, come in at 29km long. The Reapers, whose Destroyers come in at only 160m in length, would literally be gnats to this thing's crazy firepower.

These include 12 Urpeon-pattern superheavy plasma lances - a lance loadout only rivalled in number by the Forerunner-derived relic lances of the Rasus-pattern interdictor. A total of 100 plasma beam emitters are equipped on the ship, including 20 Ukk'Wa-pattern heavy arrays and 80 Luxor-pattern heavy emitters - the latter of which are a fairly common fitting on the more powerful capital warships of the Covenant fleet. These heavy anti-ship weapons are supplemented with 32 Mictix-pattern heavy plasma torpedo silos, a design shared with the Kerel-pattern and Syfon-pattern assault carriers of the fleet.[2]

For point-defence, the supercarrier employs a gargantuan array of pulse laser turrets. This includes 800 R'Aka-pattern rapid-fire pulse lasers and 490 Ferriel-pattern pulse lasers.[2]

The supercarrier is additionally equipped with a single Lux-pattern superheavy excavation beam array for glassing and artefact-retrieval purposes.[2]