Playing black-red comes with certain disadvantages: You can’t counter the Shivan Meteor, and you can’t prevent the damage. You could gain some life to offset the 13 damage, but you don’t have anything that would give you that lifegain right now.

The only thing you can do, it seems, is take the most drastic option: That Shinka Gatekeeper has to go. You just have to figure out a way to send it gently into that good night.

1. Tap two mountains to add RR (both used as generic mana) and a swamp and your Phyrexian Totem to add BB to your mana pool.
2. Spend 2B to activate Phyrexian Totem’s ability, turning it into a 5/5 creature until end of turn.
3. Spend B to activate Cabal Torturer’s ability. Choose to give your Goblin Arsonist -1/-1 until end of turn. Goblin Arsonist becomes a 0/0 creature and dies.
4. When Goblin Arsonist dies, its ability triggers. Choose to have it deal 1 damage to your animated Phyrexian Totem.
5. Your Phyrexian Totem’s ability triggers, forcing you to sacrifice one permanent. Choose to sacrifice your Shinka Gatekeeper.
6. Allow Ndali’s Shivan Meteor to resolve. The Shivan Meteor is countered on resolution because its target no longer exists. You survive this turn.