I play Malzahar as and offensive defender. I'll defend the bases, when they then go under and try to get me i'll use Garrison and use my combo, when my abilities are on cooldown I round around so they take max. dmg from turret. If I then see a opening a go for a base. If i get the base I either defend this base or i'll help my friends if they are in trouble. If I fail to take the base because of to many enemies i'll go back and get ready to the upcoming battle which is properly going to happen under my tower.

I start out with Prospector's Ring and Boots of speed. Thereafter I go for magic pen boots. After getting boots, I buy Rod of Ages and Rylai's Crystal Scepter. These items i buy because of the good survivability they give and they are also good at slowing enemies and spamming your abilities. Then I buy Rabadon's Deathcap for the big amount of AP and AP % bonus. Then I buy Zhonya's Hourglas, the armor is great at defending, so is it's unique passive where you are untargetable, and ofc the AP is nice. If your game is taking so long that you can get this last item i'll buy Will of the Ancients, nice AP and good spell vamp, so you are able to stay longer in fights. The aura is ofc also a nice bonus.

I pick Ghost because I prefer to be able to move quick to rescure a base or quickly capture a new. Ghost can also be used to catch up on a kill or flee from death.

I also chose Garrison, because of my playstyle with Malzahar. I play Malzahar in a quite unuasual way, I go alot for defending. But with this you can also go much offensively. With Garrison it's easy to defend a base get down the attackers and move onto attacking a new enemy base.

I'll go up in 21-9-0.
I take the 21 points in offense because of the nice dmg output you get from this. The 9 points in defense I take because of the great durability you get from these. These will make you able to take less dmg and maybe that will do that you win the fight, instead of the enemy.

I'll go for flat AP in quintessence, seals and glyph because of the nice start ap that are necassary in Dominion for wining the early game and start out with getting 3-2 turrets or maybe 4-1 if you are lucky and good.
For my marks I choose magic pen runes ofc because it'll reduce the dmg they will reduce from your abilities on them.

This is the way I play Malzahar, ofc it's not the only way to play him, but it's my personel favourite way to play him. In this way you can stay long in fights and do alot of dmg. You are also very good at capturing and defending bases.

Hope you could use my help, if any questions just write to me.
Have fun and play good!