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Malzahar can end up being one of two things in a game: really squishy and a negligent threat, or one of the best harassers and nukes in the game.
-Great harasser and farmer
-Very strong lane presence
-Not really any escapes
-Ultimate has very short range
-Countered by Ryze
I try to get mid every game. Your number one priority is to not get caught behind in levels. You need an excellent early game for Malzahar to be any good to your team at all in the late game. Malzahar can easily take mid and can press most other champions back to their tower (not really Heimer...). You need to farm like crazy with Malzahar, and Malefic Visions makes it easy. You can last shot almost all creeps in a wave with it. Malefic Visions is what makes Malzahar such a good early game farmer. You'll usually find yourself low on mana, but you get it right back if your Malefic Visions is allowed to travel through a whole wave of creeps. Some people still don't know how Malzahar works so they usually get caught with the Malefic Visions on themself. When you get to level 6, you can usually catch whoever you're laning with off guard and catch them with a Malefic Visions/Ignite Nether Grasp for a quick kill. Watch out for when your voidling is ready to be summoned because he does nice damage and really helps out with the gank. If they're playing cautious, continue to keep pressing them back into their tower until it goes down.
In the event that you don't take mid, that's also not a problem. Malzahar has good synergy with many other champions. Malzahar tends to last hit most creeps though, so keep an eye out for your lane partner and let them get some kills too.
In mid game, your job is to help with ganks. Malzahar is great at this with his ultimate. Usually you should never engage a fight alone with Malzahar, but if you're fed you can easily destroy most champions with your ultimate. Don't let opposing champions catch you by surprise, because at this point you're still a glass cannon.
Call of the Void is one of the strongest harassing spells in the game. It deals a lot of damage, has a long range, and silences so the person who gets hit has no chance to counter. It can help team members live and can help push your team through a guarded tower. Use this move A LOT after early game (when you're not mana hungry anymore). Usually it takes a huge chunk out of enemy champions' health if you have enough AP.
In late game, your job is to be a team player. Stick with the group and don't go off by yourself. You can keep enemies at bay with Null Zone and can sometimes catch them with a Nether Grasp while they're standing in it. Use Null Zone to look through bushes before you head into them. I've caught many people like this and killed them before they could ambush me. At this point you can spam your spells without worrying about mana. Watch for enemies trying to engage your group and punish them if they do with Malefic Visions/Nether Grasp combo while your team pounds on them.
Items.. YES I AM AWARE I HAVEN'T FINISHED MY ITEM BUILD. The items you get all depend on how the game is going. Start out with Sapphire Crystal and a couple of health potions. The Sapphire Crystal works best because the larger mana pool allows you to harass at low levels at the start of the game. From there I always go for Tear of the Goddess. This item is key to doing well mid game, you can't let yourself go oom. I always follow that up with either Boots of Swiftness or Sorcerer's Shoes. If you're having trouble taking down champions because of their magic resist, get Sorcerer's Shoes. If not, go ahead and take the Boots of Swiftness, you'll need it for situations where you need to put one last DoT on a champion and you run faster than them so it all works out. If you're doing well, pick up Mejai's next. If not, keep going for Archangel's Staff and don't even bother getting Mejai's, it would just be a waste. Next you should get the Deathfire Grasp. The 15% cooldown reduction is needed for late game. It also has a very nice active attack. Try using it right after a Nether Grasp to finish somebody off. Items after this really just depend on preference and the conditions of the game. I like to pick up Rod of Ages for games I know will last a long time and sometimes I pick up Will of the Ancients to boost my team.
For summoner spells, I always pick up ignite and ghost. Ignite has earned me a first blood many times when I couple it with Malefic Visions. It's just an extra DoT to add to your perceived "nuke" that's actually just many DoTs at the same time. Ghost will be your only escape mechanism besides blowing Nether Grasp for a stun. I mainly use it to chase down enemies to land another Malefic Visions on them for a kill.
Malzahar takes a while to master. It's hard to set up a kill and yes, it can be annoying to be such a glass cannon. I think what he brings to a team fight makes him a very valuable champion and one to be feared.