This is the original, team-based Wave Defense mode -- five players, two of your strongest ships each, working together against a shared threat. It's a different mode from Solo Wave Defense, which reintroduced the concept as something one player can run alone; if you're looking for that version, see the Late-Game Solo PvE guide linked below. The mode you're reading about here unlocks at Ops 30 and needs four other commanders (they don't have to share your Alliance) to actually run.
Section 31 -- a faction introduced alongside this mode -- is defending its own interests within the Federation, and it's asking for your help. Your team of five assigns two of its strongest ships each and defends a Central Entity (CE) against escalating waves of hostiles. Wave Defense launched with two kinds of CE -- an S31 Covert Base and a Borg Research Lab -- spread across 25 systems. Getting into the mode at all requires The Facade, a building that unlocks at Ops 30 alongside the mode itself.
Hostiles spawn in fixed locations and advance toward the Central Entity; if enough of them reach it, the run fails outright. You win by clearing all planned waves while keeping the Central Entity intact and at least one team member alive -- lose all five members or lose the CE, and the run fails instead. Rewards scale with how far you got: if your own ships are destroyed on wave 1 but your team pushes through to wave 4, you still get rewards for those 4 waves. The one hard cutoff is the very first wave -- wipe there, or lose the CE there, and nobody on the team gets anything. A full run is 10 waves, and you can't repair ships while a Wave Defense is in progress, so what you bring in is what you're fighting with for the whole run.
Every wave gets harder than the last. The baseline enemy mix is Federation Explorers, Klingon Interceptors, and Romulan Battleships, and depending on the Wave Defense's level, you'll also run into Swarm, Borg, Actian, Species 8472, Hirogen, and Texas-class hostiles layered on top. Since no single ship counters all of those cleanly, the team needs to coordinate who's bringing what rather than everyone showing up with the same loadout -- and once an enemy ship gets close enough to the Central Entity, you lose the ability to attack it at all, so positioning and timing matter as much as raw strength.
Runs launch from inside the Central Entity itself, and Section 31 Ciphers are the currency that gets you in. You can technically start without a full five-player team, but it's not recommended given how quickly the later waves scale. The countdown either runs out on its own or the team leader can start early. If you're joining rather than leading, your ships need to be docked first, then you travel with them to the Wave Defense system -- whatever's in-system when the timer hits zero is the full roster, and no one else can join after that point. In System view, the mode's icon changes to tell you the state of a given Wave Defense: ready to start (and whoever tapped it first is the leader), waiting on more players to join, already part of a team waiting to launch, in progress and closed to new joiners, or a run you're actively a member of that you can check in on even after your own ships are gone.
Two new Terran Empire-themed Wave Defense encounters have been added, spanning Ops 40-50 and Ops 50-65+, sitting alongside the existing WD locations rather than replacing them. Their directives -- Section 31 Mirror Ciphers -- come from the Mirror Refinery rather than the standard route, costing 1,500 Section 31 Credits for enough Ciphers to launch one Wave Defense every 3 days. A successful run at these new encounters can drop Liquid Trellium and a new currency, Section 31 Mirror Credits, both exchangeable for an updated rewards list in the S31 Faction Store -- including the Agony Booth and Tantalus Field Forbidden Techs, shards for a new Field Repair officer ability, and Elite FKR Reputation and Syndicate XP bundles. The Agony Booth focuses on PvE: bigger Apex Barrier against non-Armada hostiles, positive FKR reputation gains, and more Hull Health and base damage. The Tantalus Field is built for PvP instead, adding Hull Health, damage, Isolytic Damage, and Apex Barrier specifically against other players. Field Repair itself heals 25% of a ship's max Hull Health outside of combat -- you get one free activation a day (capped at 10 banked) via a free WD Store bundle, with a cooldown that starts at 10 minutes and drops by 20 seconds for every ship tier you've unlocked.