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Not Updated For Current Season
The masteries shown here are not yet updated for the current season, the guide author needs to set up the new masteries. As such, they will be different than the masteries you see in-game.
Malzahar isn't the easiest caster out there but, once you've got a good build and get his play style down, he's really fun to play as. I made this build to help those who know what Malzahar's strategies, combos and overall playstyle, but still need a build to get them over Malzahar's weak-spots and essentials.
Now with Ghost and Clarity, i can keep my distance from enemy champs in a lane, and i can keep my abilities ready. Now i use ghost because it can get me across the map and help me escape when low on health. However, you can switch ghost for flash if you prefer, as long as you have an escape spell. Clarity helps you lane longer so you don't have to recall due to low mana and, with the my masteries, it can also help as a support spell for the other mana using champions.
For masteries i went with the common caster 9/0/21 masteries, but i used two of them to enhance both Ghost and flash. I did these masteries so i can have that magic penetration in offence, and the speed, mana regen, experience, and cool-down reduction. The masteries that enhance Ghost and Flash just allow for a faster Ghost, a more supportive Clarity, and a quicker Flash regen. If you want you can take out one of those summoner spell masteries and move some where else in utility, but i have them so i don't have to change my materies just so i can use ghost one match and flash the next, because that's just a pain in the butt.
Malzahar's recommended really aren't far off to what you want with Malzahar. Now first, I didn't put health pots on because i don't use health pots, but i suggest you use health pots mainly due to the amount of lane time you can increase with it and your survivability will obviously go up. Doran's ring great starting item and it can be sold to make room for banshee's veil. Sorcerer's Shoes and Void Staff to get that essential mana penetration. Crystal Scepter to get some ability power, that slow on you abilities, and some health to fix that minor squishiness that tends to become a problem at times. Here's where i branch away from the recommended items. I get a Lich Bane to get some mana, movement, and magic resist, plus it gives you that attack damage boost after using an ability (Which is great for those champs that just need that one hit to take 'em down). Next i Build a Sunfire Cape, be sure that if you only have one slot available get Giant's belt first. This almost fully fixes Malzahar's squishiness problem. I get Banshee's Veil last because it helps me most with those long matches where, by the end, most champs have their builds completed and their abilities fully leveled. You don't want fully leveled abilities that are more than likely buffed with ability power, and banshee's veil helps with that.
Little tweaks you can make
I've noticed that I tend to tweak my build a bit so I can have a better advantage. I already went over tweaks in the masteries, but i would like to go over some tweaks in the items that can be made for special occasions. First, if you're in a game where either the other team doesn't have any casters (it happens) or your biggest problems come with fighter or DPS champ on the opposing team, you can switch Lich Bane with Frozen heart to get some armor instead of magic resist. another tweak you can make is with Sunfire Cape. If wanted, you can grab Will of the Ancients instead. Wills of the Ancients gives you and your allies spell vamp which can bring your health back up a good amount when using Malefic Visions on a minion wave.