The Nexus is the 31st and last level of Quake 4 singleplayer. It is the final part of Operation: Last Hope, resulting in the destruction of both the Nexus and the Makron, depriving the Strogg of their leader and their communication network.
In this level, Kane enters the very room that houses the Nexus, a device that links all Strogg to the Makron and enables them coordinate all of their troops most effectively. However, the current Makron has been watching Kane's advance and now enters the room to defeat Kane once and for all. After Kane has successfully slain the Strogg leader, he takes on the Nexus itself, eventually destroying the large organic brain.
This level is one of the simplest Quake 4 levels regarding the objectives: enter the Chamber, kill the Makron, wait for the Nexus to emerge and empty your Dark Matter Gun on it.
You will start on a long corridor loaded with ammunition for all of your weapons. Reload everything, gather as much ammo as you can, switch to your Dark Matter Gun and enter the next door. You will notice a large pit in the middle of the room, surrounded by four pillars. Suddenly, the Makron climbs out of it and the door you just passed through locks itself. Immediately open fire and move around the room to avoid the Makron's attacks. Sometimes, he will spawn all kinds of enemy units. Engage them only if they're really annoying you and concentrate on the Makron. Use Machine Gun or Shotgun against them to save ammo for stronger weapons for the Makron. After you have drained his energy for the first time, the four pillars recharge him and his upper body detaches from the legs and you will have to defeat his second form. Get this part done ASAP, since he may fly to one of the columns and grab a torso power unit to regain energy. You can destroy the torso unit by shooting at it, keeping the Makron from restoring his health. If you run out of ammunition for your Dark Matter Gun, use your Rocket Launcher or the Nailgun (as a last resort).
Note: Save some ammunition for Dark Matter Gun if you can, it will make the final battle easier; by this stage of the game, you should have plenty.
After you have killed the Makron, the pit will open up again and reveal the Nexus' organic brain. In addition to this, teleporters will appear in every corner of the room. Use them to reach the second floor. Here, you can use two Stroyent Health Stations if you're low on health. Now, you have to deplete the Nexus' shields before you can damage the brain itself, and to do this you must shoot the top of the machine, above the 'brain'. The best weapon to take down the shields is a salvo from your Rocket Launcher. When damaging the brain, use your Rocket Launcher, Lightning Gun or the Dark Matter Gun. After a while, two Repair Bots will enter the room and fix the damaged shield generator, causing it to resume function, but it is possible to keep damaging it while the shields are regenerating. Even though the Nexus has no weapons of its own, it will keep spawning Strogg units into the room, so shooting them is pointless. To avoid fire from Strogg units on the first floor, never remain on the energy bridges on the second floor.
The destruction of the Nexus triggers a cutscene that shows Kane leaving the Nexus and returning to the Hannibal.
When you fight the Nexus, the fastest way to bring it down is to equip the dark matter gun and not to shot on the nexus directly. The Dark Matter Gun has a large area it damages, so you have to shoot left or right of the nexus. You have to miss it, so the projectile of the dark matter gun can continue dealing area damage even when it passes the Nexus.