Cortex Command was a part of the original Humble Indie Bundle. It was also a bonus game in HiB 2. Can’t remember if it was in HiB 3 but Steam activation keys have been added for anyone that purchased the first two bundles.
Just log into your bundle page and click on show activation keys.
You’ll see a key specifically for Cortex Command. Best way to get to your page would be by looking for the confirmation email with your unique link.