The Makuta of Karda Nui died in the Energy Storm, but they can teleport and and I believe they have the power to pervade their bodies. Why were they killed?
Even if they did escape from the Energy Storm, they will still die from Teridax since he doesn’t want any competition. 
Antroz, Vamprah and Chirox were blind so teleporting to a specific place might have been difficult for them. (In the book Antroz needs multiple teleportation steps to reach Mutran after he abandoned the Jetrax which indicates a certain problematic of blind teleporting to me) Also Antroz asked Bitil to help them escape.
Gorast didn’t even try to escape.
And Bitil actually tried to teleport, but the energy storm interfered with this somehow resulting in his teleportation power not working.
As to why they didn’t simply made themselves intangible… the energy storm probably still would have hit them. The Makuta would have been able to reduce their own density, but only to a certain point.
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Iirc, most can’t teleport through the walls of Karda Nui.
But they can teleport too the subway?
I understand. The blind ones are not able too Teleport correctly.
Mutran was too crazy too flee and Gorast was just too shocked. But Bitil just fly
Correct, only Artahka’s unique form of teleportation can pass through Karda Nui’s walls.
They were stuck basically. It was a trap, with no way to escape in time.
But Bitil can teleport too the end of the wall and try too get too the Exit, they use too reach Karda nui. Right?
And the energies of the storm merged with his teleportation power, litetrally overpowering and perishing him, as seen in the Comic. (Mata Nui Rises, I think?)
Mutran tried to control the storm, but it was more powerful than his willpower, and got perished by it. Gorast was shoked that Icarax & Krika were right, she didn’t even try to escape. Antroz, Vamprah and Chirox were already blinded, they couldn’t see where they were gonna teleport, so they were doomed.
And in the Makuta’s Guide, Teridax mentions that he sent his most powerful Makuta to Karda Nui to die for they were the ones, who most likely would have attacked him on the same way as he attacked Mata Nui.
According to Legends 11: the Final Battle, Bitil tried to teleport but couldn’t due to the energies of the storm.
~W12~
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I think the radius Karda Nui is such a grand distance, and the storm built up so quickly, that Bitil would not have had time to escape, even if the storm hadn’t interfered with his teleportation. As for shapeshifting, well, the Phantoka were blind, yes, but no form could prevent them from being decimated by the lightning spears. As we aren’t aware of the nature of the Makuta’a teleportation, we have no idea as to how easy it would be to teleport to the exit of Karda Nui. Antrim took numerous jumps to reach Mutran, and this might have been because Antrim couldn’t teleport very far at all.
Antroz were blind, that was the reason why did he teleport such small distances. But Teridax could teleport Vakama from Ta-Metru to the “Maze of Shadows” (tunnels above Metru Nui)
…and just saying…The makuta teleport themselves to places when they had to travel long distances, but they used a gate to reach Karda Nui, because they couldn’t teleport inside the core.