Not Updated For Current Season
To start off as Malzahar I like to get an amplifying tome and health pot because it allows you to build SS asap. To me this is very important because malzahar is great for ganking after level 6. The reason I start off with Call of the Void is for voidling purposes. While in spawn I always cast Call of the Void to charge up my voidling. I find that this helps with early pushing in mid but it is just a personal preference. In my opinion the Malefic Visions is not as effective at killing minions or harrasing as Call of the Void at the start of the game.
The runes I choose to use with Malzahar are fairly standard for all mages. The magic penetration runes are important just for extra damage. The CD reduction I think is very useful for spamming skills a little bit faster and improves farming, since Malzahar is a great farmer throughout the entire game. To go with the skill spamming I feel it is necessary to have that extra mana regeneration. The Quintessence's I have chosen are based on the players playing style. Personally I invested in health Quintessences because Malzahar is fairly squishy and they are also universal runes that are good on any hero, however; they are quite pricey. The other alternative is magic penetration Quintessences for aggressive players that like to play on the edge and are always looking for that first blood.
The masteries are pretty standard for any mage champion. The basic 9/0/21 can be changed around slightly depending on the summoner spells that you choose. But otherwise nothing else should be changed.
Starting off with an amplifying tome gives you the ability to get SS asap. This is a key item for Malzahar. Since Call of the Void and Null Zone are Aoe abilities, this give you the potential to get many kills and assists in team fights, thus, increasing yours stacks. If you don't like using SS the other option is a ROA. This is a good item to buy because it makes Malzahar a bit less squishy, also if u are having a bad game it is a bit of a waste to have a SS without any stacks. The other items are just the ones I like to use in order to stack AP and magic penetration. Also the extra mana from AA is useful when spell spamming. Although, these items can obviously be substituted for different items such as Deathfire Grasp, for example, if the other team is composed of a lot of high HP champions. Also, Zhonyia's is usually a good item to get because of the high AP and armor and the ability is very useful because malzahar tends to get focused down quickly in a team fight.
As I said before, I like to charge my voidling at the start of the game by using Call of the Void in the spawn. From then on maxing Malefic Visions is the main priority. It is does good damage on champions and it is perfect for farming. The extra mana that you get back from killing minions is very important so always remember to focus down the minion with the dot with your auto attacks. Maxing out Call of the Void is your next priority because it can be used to quickly wipe out large groups of creeps and it can be a good way to nuke enemy champions. Null Zone is a great spell. I choose to get it in the late game because it does more damage to champions with more HP. It can be extremely effective at taking down tanks or high HP champions and is great for teams fights due to the Aoe. It is also a great idea to Null Zone first and then Nether an enemy inside the circle. This maximizes your damage and allows your to take down almost any champion in a solo fight (assuming you have enough AP).
Flash and Ignite are by far the best summoner spells for Malzahar. Flash can be used defensively or offensively. You can use it to flash through walls or up ledges to get away. Also flash works really well when trying to nether someone. You can easily catch someone off guard when laning and get a easy kill. You can also flash and nether when chasing to finish off the fleeing champions. Since Nether Grasp is a channel spell, this allows you to use ignite while channeling. This makes you the much more effective and in combination with Malefic Visions squishy champions have little chance of surviving.
All in all, Malzahar is indeed a very deadly champion no matter how you play him. He can be effective in both middle and side lanes as well. His amazing farming abilities makes him a good mid champion. Also, Nether Grasp is most effective in the side lanes. When used at the right opportunity Nether Grasp almost always ends up in a kill (building those SS stacks :P). Please make any comments below because I would be glad to here any suggestions on minor changes that you may have.