The Nexus: The Eye of Eternity

Malygos' lair can be found in the Nexus, behind the top entrance. Time to watch the light show...

Abilities

Phase One:

Arcane Breath (Arcane) - Deals massive Arcane Damage to targets in front of Malygos. After 5 seconds, everyone hit will explode doing more Arcane Damage.
Arcane Storm (Arcane) - Multiple missiles hitting random people for Arcane Damage.
Vortex (Arcane) - Caughts people in a vortex dealing Arcane Damage, casting is still possible.

Also there are Sparks appearing the fight that you can kill to gain the following buff:

Power Spark (Buff) - Increases damage dealt by 50%.

Phase Two:

Arcane Bomb (Arcane) - Knocks targets back and leaves Arcane Residue (large bubble) giving you the following buff:
Arcane Overload (Buff) - Reduces Magic Damage taken by 50%.
Surge of Power (Arcane) - Raid wide Arcane Damage every second. Stand in a bubble.

Also there are multiple Nexus Lords on discs:

Arcane Shock (Arcane) - Blasts an enemy with Arcane damage, stand in a bubble. Can also be reflected.

Phase Three:

Static Field (Arcane) - Summons a field of cracking energy dealing Arcane Damage to everyone nearby.
Surge of Power (Arcane) - Deals 72k Arcane Damage over 3 seconds to 3 targets (same spell, different effect).
Arcane Storm (Arcane) - Fires missiles at random drakes.
Arcane Pulse (Arcane) - Lots of Arcane Damage to drakes within 30 yards range.

Also you will fly a drake, which has the following abilites:

Flame Spike (Fire) - Fires a Fireball at Malygos, awarding one combat point.
Engulf in Flames (Fire) - Puts a fire DoT on Malygos, the more combat points the longer the duration.
Revivify (Heal) - Puts a HoT on the target, awarding one combat point.
Life Burst (Heal) - Puts a HoT on everyone within 60 yards, heals for more and longer the more combat points are available.
Flame Shield (Buff) - Puts a shield on you, reducing damage by 80%. The more combat points the longer the duration.
Blazing Speed (Buff) - Incrases flight speed by 500% for 8 seconds.

The following tactic has been written by Lancar:

Class requirements

1 Tank, and preferably 2 Death Knights but if you can only get one then that works too.

The pull

The encounter doesn't start until someone uses his/her Key to the Focusing Iris on the central orb. Just click it and Malygos will fly down and engage the raid. It is preferable to do this when he's on the south side of the "room" so he'll face north when he has landed.

Positions and strategy

This fight is divided into 3 very different phases, making this encounter the most varied one in Wotlk as yet.

Phase 1: Malygos on the ground

Since Malygos is a dragon he will use breath attacks on anyone in front of him. Standard dragon flighting tactics work well here, but with the added bonus that he doesn't use tail whips and so it is safe to stand behind him. He'll also occasionally use Arcane Storm to randomly hit people in the raid.

The MT aggroes him, and have him face somewhere north while the raid stays south.

At regular intervals he will fly up and catch everyone in a big whirlstorm, doing damage over time to everyone. There is no way to escape this storm before it's duration is up, however all instant attacks and abilities work so you can continue to attack and heal while inside it. When the storm is over, everyone will be dropped in the middle of the room.

Unless the MT says otherwise, head south now because the MT will face him north and getting cought in a breath attack is fatal.

What's special in this phase is the glowing Sparks that regulary spawn out of rifts off the sides of the platform. These will head unerringly towards Malygos, and if they reach him he'll get a +50% damage buff, which thankfully has a somewhat short duration.

While the sparks are immune to all forms of aggro, they are susceptible to CC and thus can be slowed, frozen or thrown around. Killing the spark will yield a patch of electrified ground undearneath it that will, instead of Malygos, increase your damage by +50% so long as you stand on it.
It is the DK's job to make sure that the sparks are continously killed on the south side of the platform, and on top of eachother, so the damage buff will stack.
Granted this isn't always possible due to random chance and human error, so the MT will have to move Malygos around to make sure he's always in the best position to strike at from the patches of electrified ground.

At 50% HP, phase 2 will start. Keep DPSing him while he's chatting. The more you shave off him now, the less you'll have to deal with in phase 3.

Phase 2: Malygos' servants

After he has flown off, several of his servants will fly in on hoverdiscs. Some on near the ground which follow normal aggro, and some circling the area in the air while bombarding random people with arcane barrages. The ones on the ground will immediately aggro anything on the platform with just a tiny bit of threat, so make sure you don't use any abilities until they've been picked up by the tanks.
Killing one of them will free up his hoverdisc, which can then be mounted and used to fly up to the enemies above and engage them. Only melee DPS should do this, as ranged DPS can still hit them from the ground.

For the whole phase, magic shield bubbles will spawn somewhere on the platform. It's very important that you are always protected by these bubbles, as they'll halve any arcane damage taken... and you'll take alot of it, trust me.

Don't think Malygos has left you, though. He'll fly in and blast the whole arena with his breath attack every now and then, after giving a short emote. If you're not in a bubble when this happens you will take massive damage.

Killing off all the enemies will cause Malygos to get really pissed, making him break apart the whole area, thus sending everyone falling. Thankfully, Alextrasza's red drakes catch you and phase 3 starts.

Phase 3: Sky High

Arguably the most difficult phase to master, this one is fought completely on the backs of the red drakes. They have 6 abilities, explained in the listing above and the picture below, but you only ever need to use 3 of them.

Nr 1 & 2 are the DPSer skills, and 3 & 4 are the healer skills. Both roles function pretty much the same way. Using the first skill will award you with a combo point, and the second skill will turn all your points into a a damage- or heal-over-time effect. Ability Nr 5 is the Shield, which will turn your combo points (no matter which type) into a protective barrier to shield you from damage.

Malygos will continously charge a ray attack that will hit 3 random people in the raid. Unless you have the total devotion of a healer at that point, you'll likely die from that, but you can protect yourself from it by popping up the Shield just before the ray is fired at you (watch Malygos' castbar. Enable it in Interface options, if you haven't already). You'll know if he's gonna hit you next since you'll get a warning saying "Malygos fixes his eyes upon you" or something similar.

There will also be arcane pulse clouds spawning which will hit everyone in it for about 10k damage.

The trick here is to continously put new DoTs on malygos while always being ready to pop your shield if he is about to shoot you. The DoT's stack infinitely, so the more you put on him, the more damage he will take. When a storm hits, move in a clockwise circle motion around Malygos until you're out of it, but STAY with the group. It is very important for the healers that you do since they cannot always look after any single person and will instead rely on their AoE heals (ability 4, Revivify) to take care of most of the raid.

The healers heal, all others take a DPS role.

For the DPS, a rotation of 1 - 1 - 1 - 2 may be best, since it will allow some time to pop a shield if you get "watched". The more combo points you use for the damage-over-time ability, the longer it will last.

Malygos has an enrage timer, so if you take too long in phase 1 & 2, you will not have enough time to finish him off in phase 3. Don't give up if he goes Enrage at only a few % HP, however. Since the DoTs stack, the damage he takes will incrementally rise the longer the fight lasts and towards the end, his hit points will literally be burning off.

Note:

You are encouraged to do the quest "Aces High", starting with another quest in the Transitus shield outside the Nexus (It becomes available when you hit lvl80). This quest will have you use exactly the same type of drake which is used in phase 3 of Malygos, so it'll be valuable training.

Normal Difficulty

There will be much fewer enemies in phase 2, and he'll only hit 2 people at a time in phase 3.

Boss Kill: