Anti-Muta Play (PvZ)
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Mutalisk play is increasingly popular in ZvP, and dealing with those mass Mutas is a common PvZ problem. Going for a 2 base all-in to try to kill the Zerg before or right as he gets Mutas is certainly a viable option but that is dodging the problem, rather than dealing with it. This page outlines how to play a long macro game against mutas.
Beat a Zerg going Muta/Ling in a macro game.
 Basic Build Information
Builds that blindly mass Sentries at the beginning are bad, particularly if the Zerg is going Mutalisks. Getting to 8-12 Sentries early game seems to be very common in PvZ but it is often not a good idea, unless going for a quick 2 base all-in. Guardian Shield is great against the bounce attack of Mutas, but the Sentries will often be sniped quickly, resulting in just a huge waste of gas that could have been better spent on additional Stalkers and HT. (Sentries are also ineffective against Infestor/Ling play, Baneling play (with Overlord drops), and any more than a moderate amount (like 4-6) will be a waste against early 2 base Hydralisk play. Start with 2-4 Sentries (n.b. this is starting with a FFE, so if you're Gate expanding you could use a few more) and only add more if you scout Roaches.
The core of the anti-Muta army is Blink Stalkers, not Phoenix. The Protoss opening does not matter much, far more important is the reaction upon scouting Mutas. If you were planning to go Colossus and already have a Robotics Bay, that's fine. Just do not make/cancel Colossi, add a Twilight Council, and research Blink as soon as possible. If you went Stargate, it's fine to continue making Phoenix to help counter Mutas, but you still want Blink, so get the Council as soon as possible. Basically, no matter what your initial gameplan, as soon as you see Spire/Mutas your immediate goal is to have Blink with at least 6-8 Gateways on 2 bases.
 Unit Compositions
Phoenix are great against Mutalisks in low numbers. However, trying to transition into Phoenix if you don’t already have a Stargate is too late since you will never be able to match your opponent's production. By the time you get out a decent number of Phoenix he can have 20+ Mutas. While you can theoretically kite him forever, every slight mismicro you commit will result in losing a Phoenix or 2. If you already have a Stargate from the opener, then it is ok to make some Phoenix to help deal with the initial harass. The micro dynamics still suggest that it is unwise to use Phoenix against mass Mutalisks. If you’ve opened dual Stargate and your opponent goes Muta, then it should be an auto win. Simply build Phoenix and crush the Zerg.
The ideal composition to battle Muta/Ling is Blink Stalkers, Zealots, and High Templar. Keep a High Templar at each base with a few in the main army. As the game progresses and more Mutalisks enter the fray, it is appropriate to increase the HT count, but the Stalker count must be kept high. Do not morph Archons preemptively (make Archons after using Psionic Storm, not before). Though Archons are comfortingly sturdy, it is better to have Storm than Archons, and Stalkers are too important to afford both. Sentries - for Guardian Shields against Muta and Force Fields against Zerglings - have some value, but are rarely worthwhile since they are easily sniped. Zealots are important not only as a mineral dump, but also to protect Stalkers from Zerglings and conserving Storms for use against Mutas.
 Establishing a 3rd Base
It is difficult to secure a 3rd base with Mutas and Lings harassing everywhere. However, the seemingly contradictory answer to this is to try to set up that 3rd earlier. The later you try to expand to your 3rd, the bigger the Muta ball is and the harder it will be to safely establish the 3rd base. If you attempt to expand where there are only a dozen or so mutas in the muta ball, it takes a while for the Mutas to actually destroy the Nexus warping in, thus there is some time to get Stalkers there to defend. But when the Muta count grows to 20 or 30 Mutas, they can do a much greater amount of damage in that same time, perhaps forcing a cancel.
By the time you’ve scouted the Zerg going Mutas, if you’re not going to 2 base all-in the Zerg, and you’ve started Blink research (yes you can and should start trying to expand before blink finishes), have a few cannons in your mineral lines, and have some Stalkers out to chase away Mutas, you need to start trying to take your own 3rd. It’s ok if you start the Nexus and Pylon but then Mutas or Lings force a cancel. The expansion is a low risk/high reward tactic, if he forces a cancel you only lose some minerals, not a big deal since the gas is what's valuable.
Remember: Muta/Ling is weak in a straight up fight. Against standard Roach play, expanding to your 3rd too early leaves the Zerg an opening to attack and kill you; but when the Zerg goes Mutas, their army isn’t as strong and you're safe to take a fairly fast third base.
 HT vs Archon
As the Muta flock grows bigger, even a mass of Blink Stalkers will be insufficient, and Protoss must add a Templar Archives. Often, Protoss will make Templar just for Archons, but doing so eliminates the option of Psionic Storm, the ultimate weapon against Muta/Ling. Archon splash is small and can be combated via magic box, and their attack cooldown is not that great, so when the Muta flock gets really big, Archons can be picked off after getting in only 2-3 shots. Meanwhile, Storm has a much larger radius, a much larger range (9 vs 3, especially important when defending against harass), and Storm keeps working even after the HT dies (and the HT will die, because Mutas will pick them off, but hopefully not before you get off the Storm and deal 20-60 damage to a big portion of the flock). As for Zerglings, you have Zealots to counter those. You shouldn’t be relying on Stalker/HT/Archon to fight against Zerglings.
There are 3 situations when you want to make Archons:
- After you’ve stormed. Mutas usually target HT as their first priority so it’s rare for a HT to live long enough to gather energy for another Storm.
- You have 2 or more HT near each other, Mutas have spotted them, but you don’t have energy for Storm.
- For some reason you have a ton of gas and not a lot of minerals. If you have a ton of gas AND minerals then your macro sucks and you should just make more Stalkers. But it’s not uncommon for the Mutas to have done enough economic damage that you end up starved for minerals but with a lot of banked gas. In that case, having 10 HT in your army for Storm is overkill and it’s ok to make some Archons.
 Defending Multiple Bases Against Harassment
Perhaps the most overlooked tool against Muta/Ling are Observers. Make 4-5+ of them. They cost quite a bit of gas, but there's no other use for the Robotics Facility in this strategy and the Observers are well worth it. Spread the observers around the map to track where the muta ball is at all times, then you’ll have a lot of advance warning where the Mutas will strike next, time to move Stalkers in position to defend. It can also be helpful to split your Stalkers into 2 separate groups and keep them in separate bases, but if you get the Observer network set up then it isn’t even really necessary.
You’ll need 1-3 Photon Cannons in each mineral line early on, mainly to buy time for Stalkers to get there. As the Muta ball gets bigger, you will need to leave a HT in each mining base, and stop relying on Cannons. You can add more Cannons as the Muta ball-increases in size, but it often is not worth the minerals, spend them on Zealots instead. Speaking of extra Cannons and Zealots, it is a good idea to have extra Cannons and to leave some Zealots in your 3rd, since a really common maneuver for the Zerg is to send Mutas into your main while streaming in Lings into your 3rd.
Note: rsvp prefers having more Zealots and fewer Cannons to defend each base, but it's not a bad idea (and safer too) to mineral dump on Cannons instead of Zealots as the game goes on. Having 6 or more Cannons in each base late-game can help to buy you even more time against bigger Muta balls.
 Harassing and Attacking
The strength of Mutalisk play is the ability for the Zerg to expand everywhere and keep the Protoss in your opponent's base. Most of the time you’ll have to rely on harassment via DTs or Zealots to try to kill expansions since, if you move out with your main army, Mutas will just counter into your base as soon as you leave. DTs are a bit of a gamble since they cost a lot of gas but can be really effective at taking out expansions. If you use Zealots, consider harassing with them only when there’s a battle going on or Mutas are in your base. Also, avoid Xel'Naga Towers or use a Warp Prism. The Zerg will generally have map control and there’s no point in trying to harass with Zealots while Mutas are flying around in the middle of the map picking them off.
As for actually moving out (which you will have to do eventually), in most cases you shouldn’t move out until you are maxed. Until then, do not panic, stay calm, do not feel the need to move out prematurely. It's ok if the Zerg takes the entire map, your opponent cannot kill you. Only attack when your army is big enough so that you can attack with the majority of your army while still leaving some at home to defend the counter. Usually this is when you're maxed. The important piece is having a lot of High Templar, in your army and at all your bases. If you had great success defending against Muta harass (little to no damage done, you took your 3rd decently early, and you’ve killed some Mutas), then sometimes you can move out before you’re maxed. Just make sure that you have enough HTs both at home and in your main army when you leave. Again, Storm is the key.
Stalker/Zealot/High Templar is a composition designed to go from the mid-game onward, but it is important to pay attention to possible Zerg transitions and not let them catch you off guard. This generally means having an observer either at Zerg's rally point or in their main base to check his tech. The most common transition is to Roach, in which case you should add Immortals into your army. Blink Stalker/Zealot/HT is already a fairly versatile composition, and you don’t really need to change your composition if he adds/transitions to Banelings, Infestors, or Hydras. As for Hive-tech transitions, Ultralisks can be extremely dangerous if you don’t scout them in time (if you do, add Immortals). Against Brood Lords, there’s really nothing special you have to do since Brood Lords and Mutas don’t synergize well and Mutalisks are terribly supply inefficient in a straight up fight.
- Upgrades are extremely important, including armor. Make sure to get both attack and armor upgrades against Muta/Ling. Although all the replays below are one Forge, going dual Forge may not be a bad idea.
- Keep expanding! There’s no reason to be satisfied with 3 bases. When your 3rd base is secure, start looking to expand to your 4th. Then your 5th. Don’t stop expanding, expanding doesn’t cost gas.
- When engaging Mutas with Blink Stalkers, don’t Blink into them. Walk up to them, and then you’ll be able to Blink to chase as they run away.
- Keep important tech buildings away from the edges of your base. Watch out for Artosis Pylons. There’s no need to put Pylons or tech around the edges of your base against Mutas.
- Never base race against Mutas. Sometimes the Mutas may get into a mineral line and cause some damage, and you may be tempted to just say screw it and go all-in, but resist the urge. Stay calm and focus on defending.
- Cannon placement: keep Cannons close to each other so that Mutas cannot pick them off 1 at a time. Also, build them on the side of your minerals that face the direction Mutas will likely come from, so that the Mutalisks have to get past the Cannons before they can reach the mineral line. For example, if you are at 9 o'clock on shattered and the Zerg is at 6, you should place the cannons near the bottom of the mineral patches.
- As you're getting close to being maxed, it's a good idea to add some Immortals into your army even if you didn't scout a Roach or Ultralisk transition. Immortals are extremely helpful against the inevitable Spine Crawler walls you'll have to break down.
- A note on Storming: make sure you're targeting underneath the Mutas (their shadow). Turn on the flyer helper in your settings.
- PvZ Dealing with Muta - TeamLiquid.net discussion thread (source for this article).
- PvZ: The Guide: Mutalisks
6 rsvp PvZ replays from ladder, practice, and tournament games. First 2 replays are the best. ^^