Hostiles spawn in fixed places and move toward the Central Entity. If enough of them reach it, the run fails. You win by clearing all waves while the CE stands and at least one team member is alive. You lose if all five players are defeated or the CE is destroyed. Rewards depend on how far you got. If your own ships die on wave 1 but your team clears 4 waves, you still get rewards for 4 waves. The one hard cutoff is wave 1: if the team or the CE is destroyed there, nobody gets anything. Once an enemy gets too close to the CE, you can no longer attack it.
Runs start from inside the Central Entity, and Section 31 Ciphers are the currency that launches one. You can start without a full team, but that is not recommended. The run begins when the timer reaches zero, or sooner if the team leader starts it. If you are joining, dock your ships first, then travel with them to the Wave Defense system. Every ship in the system when the run starts takes part, and nobody can join after that. You cannot start a new Wave Defense in a system that already has one running.
Every wave is harder than the last. The base enemy mix is Federation Explorers, Klingon Interceptors and Romulan Battleships. Depending on the Wave Defense level, you also meet Swarm, Borg, Actian, Species 8472, Hirogen and Texas-class hostiles. No single ship counters all of them, so the team should agree who brings what.
Section 31 is a new faction defending the Federation's interests, and it asks for your help. Wave Defense launched with two kinds of Central Entity, an S31 Covert Base and a Borg Research Lab, spread across 25 systems. Winning each wave earns Section 31 Credits, which you spend in the Section 31 part of the Faction Store. The Facade is a building that unlocks at Ops 30 with the mode. It adds damage against Wave Defense hostiles and raises ship Hull Health and officer stats. Section 31 Transmitters, sold in the S31 Faction Store, upgrade it.
In System view the Wave Defense icon shows its state. It can be ready to start, and whoever joins first becomes the leader. It can have a leader and be waiting for more players, and you are not yet a member. It can be a team you have joined that is still waiting to launch. It can have started and be closed to new players. Or it can be a run you belong to, which you can still watch after your own ships are gone.
Two Terran Empire-themed Wave Defense encounters were added, for Ops 40-50 and Ops 50-65+. They sit in the same places as the existing Wave Defense systems. Their directives, Section 31 Mirror Ciphers, come from the Mirror Refinery. 1,500 Section 31 Credits buys enough Ciphers for one launch every 3 days. A successful run can drop Liquid Trellium, depending on the wave reached, and a new currency, Section 31 Mirror Credits. Mirror Credits buy items in the S31 Faction Store: the Agony Booth Forbidden Tech, the Tantalus Field Forbidden Tech, Field Repair shards and materials (Welding Hardware), and Elite FKR Reputation and Syndicate XP bundles. The Agony Booth is for PvE: more Apex Barrier, Hull Health and base damage against non-Armada hostiles, and better FKR Reputation gains. The Tantalus Field is for PvP: more Hull Health, damage, Isolytic Damage and Apex Barrier against other players. Field Repair heals 25% of max Hull Health out of combat. You get one free activation a day through a free bundle in the Wave Defense Store, and you can hold up to 10. The cooldown starts at 10 minutes and drops by 20 seconds for every ship tier you unlock.