The X-Hunters appear after you defeat two Mavericks. They'll each appear in the X-Hunter room of a random stage. They move to a random different stage every time you clear a level or exit a level you've already cleared from the pause menu. You'll want to defeat all of them before finishing off your eighth Maverick.
Serges – Zero Part No. 1 (Head)
Serges rides a floating platform left and right. It has spikes on the side, so don't touch them. When you press the shoot button, he raises a barrier for a moment, which will block your attacks. He drops mines along the floor, which you should destroy as soon as possible, because they will limit your movement. He can leap into the air and spin, firing a wave of shots in a circle. He's vulnerable when he's in the air, since he can't raise his forcefield there. He's weak to the Sonic Slicer. If you fire it at a wall, it can bounce off and come back at Serges after he has lowered his barrier. There's also a good chance a missed Sonic Slicer will eventually hit him when he jumpes into the air.
Violen – Zero Part No. 2 (Torso)
Violen attacks with a giant ball and chain. The ball will deflect any shots that hit it. It will bounce off of the walls and floor in an arc that becomes somewhat predictable after you see him attack a few times, though not very. He usually throws it outwards, away from himself, and it will bounce around progressively shorter distances from him as he draws it back in towards himself. Sometimes it will actually bounce farther away from him, but you can't really tell this is going to happen until it happens. The fact that the way it bounces changes depending on where he is relative to the surfaces of the room, as well as just coming out in different directions even from the same starting point, makes it tough to avoid. Violen also has an attack where he shoots energy balls from his hands in a large wave. If he does this in the air, climb a wall to avoid it.
Violen has a lot of health and hits pretty hard, and his difficult-to-predict flail attack can make him a challenge. His weakness is the Bubble Splash, but that's slow and has a short range, so it's not really worth using. Just use charged X Buster shots. It's probably worth your time to use a sub tank (or more than one) in this fight, since whatever Maverick you'll fight after him is probably easier to beat than he is.
Agile – Zero Part No. 3 (Legs)
Agile is intimidating. He's very quick and his main attack is a massive, fast-moving crescent shaped beam that sweeps across a large portion of the room. His only other attack is dashing across the room with a flurry of sword swipes, which he'll only do if X is on the ground. The lowest beam attack is not too low to dash under, but you're inviting Agile to do his dash attack if you use this strategy. You'll be dashing right towards him when he decides to dash into you and damage you.
You can lock him into a particular pattern with some practice. Climb as high on the wall as you can, then immediately drop off when Agile starts his attack. Once you land (and he's just about to land), unleashed a charged X Buster shot or Magnet Mine (his weakness) and immediately climb back up to the top of the wall. You can repeat this until he's down. Agile can be tricky if you don't know this pattern, but he's not too tough if you do.