You can use Command Points to get Legendary packs and purchase Power Upgrades for your 3-star or better heroes.
When you have some, they’ll show up next to your Iso-8 and Hero Points:

You can get Command Points in these ways:
  • As mission rewards for key missions in Story events.
  • As part of placement rewards in Story events and Versus events.
  • When someone purchases certain bundles of Hero Points or Iso-8 (Logan’s Loonies, Asgard Treasure, Stark Salary, Hidden Stash, Rich Deposit, or Mother Lode), some Command Points are awarded to them and everyone else in their alliance. (If they’re not in an alliance, they’ll still get the bonus.)
  • In daily rewards.
  • VIP Membership