Let me explain the reason I wrote this build. Quite simply, I disagree with a lot of the builds, specifically Malzahar builds, out there. I realize this is only my opinion, and that everyone plays in a manner that they feel comfortable with. I feel comfortable with the play-style that will be explained through this guide. I would love to say "Comments are only appreciated AFTER you play-test this", but I don't expect that to be a qualifying reason to comment, and, likely, would not change your opinion either way.

Cons:
No nukes so to speak.
Hard to get accustomed to.
No real CC other than Ultimate.
Ult and W combo only guaranteed kill.

Pros:
Probably one of the best mid-laners.
Extremely talented pusher.
Can get multiple kills thanks to E.
Almost every spell hits multiple enemies.
Strong laning skill thanks to constant MP return.

Magic pen runes. Where do I begin? In my opinion, for many (not all) AP champions, magic pen runes are better than AP runes. I say this because with magic pen runes and rushing boots, you will do true damage to pretty much any champion you come across. This is especially important for MID Malzahars (which, honestly, is how I think he should be played, mid only). Doing true damage will help your E (which I will call his DoT (Damage over Time)) not only push through entire waves of minions with a single cast with the help of auto attacks and minions, but push your opponent back too, which is the point.

I don't think there is much to be said about my masteries. I went a simple 9/0/21. I've toyed with taking greed instead of the 3.33% less time dead, because it is just a filler spot to get me to 20 so I can get the final branch. Any suggestions would be appreciated.

I am sure this is probably the most controversial part of my build, vs. what I've seen built in the past on Mobafire. To me, the Q trick is useless. Yes, you get your minion on the first cast when you hit middle, but so what? I'd rather run E @ start. It's going to be more effective than your minion, and, if you time it correctly, can even push through a wave at level 1. Wait until your minions attack, then push with it. That's just me. Another reason I run this is because at level 2 you get your W, which will guarantee a push through a wave when combined with E (just focus on the big tank if he's running through), and probably do the initial 5% of damage to the opposing mid. To me, these are the most important skills to max. Q IS important to get early on, but only for the utilitarian use of the silence. The damage, while good, doesn't fall in line with the DoT potion of ALL HIS OTHER SPELLS. Use it, don't get me wrong, just don't try to nuke, I don't feel that's Malzahars job.

Because of your runes and masteries, I think going straight for a maximum AP build on Malzahar is enough. He isn't a CC champion, so I don't recommend getting him a Rylai's, especially because NONE of his spells (other than ult, which should be used to get a kill) give you more than a 15% slow. Not worth it, to me. If your opposing team gets smart and they get 100 or more Magic Resist, I'd sell one of the AA staves for a Void Staff. This will, when combined with your masteries, give you a 55% reduction of their MR, AFTER the 39 you have from your boots and runes.

Farming and mid-laning really go hand in hand. You can sit in mid and just spam E all day. The MP regen runes, in combination with your E's MP restore per kill effect, will make it so you can sit in your lane FOREVER. Remember, because your spells stay out and last a good period of time, you have really no reason to be harassed by enemy teams. No matter where you are on the map, if your DoT kills a minion, champ, what have you, you'll get the gold (and I believe EXP) for it.

Additionally, though this is technically telling you how to mid, not farm, despite the title, your E should not be solely used on minions. In situations where your minions have pushed to the tower (it should happen frequently), don't waste your E on the next wave of minions unless the enemy champion is mia. Instead, throw that DoT onto the champ, just remember if you get into the turrets range at any point after that, it will attack you. Try a E -> Q -> W combo if you're confidant. You'll do massive damage to the enemy, and almost instantly (if placed smartly), get out of turret range so it won't hit you.

In team fights, Malzahar has a different job than just throwing his E to push through minions. Save your E, first of all. You're going to want to W -> R onto whatever opponent your team has agreed is the biggest ... nuisance. Usually a carry. REMEMBER, when people say "Don't focus the tank" that applies to anyone BUT Malz. He can easily solo a tank with a W -> R combo. However, don't focus if you're not good with the combo yet. Anyone caught in that SHOULD die, regardless of HP, because with this build you'll do somewhere in the ballpark of 15% of their HP/sec. that's 60% of their HP if you manage to keep them inside. Save your E to throw it on them AFTER your combo ends, if they survive. I say this so it will transfer to another enemy nearby that runs to cover them. You can then jump in and kill this person too. However, if there is a carry on the enemy team that is fed, or doing most of the damage to YOUR team, take them out of the fight with your ult.