Alter Ego is a minigame similar to hackathon in Sly Cooper: Thieves in Time. Two player co-op is available.
In all of the Alter Ego levels, there are little goo minions, and there is a boss called "the Gate Guardian" in the firewall Bentley hacks. There are also purple walls which you must shoot multiple times to make disappear, and also regenerate.
- Purple Nano-bot - The Core sends a Goo-like minion to kamikaze Bentley and take away some health.
- Translucent Nano-bot - The Core sends a Goo-like minion to kamikaze Bentley and take away some health. These types are transparent, they shoot small lasers, and are easy to overlook.
- Purple Goo Nano-canon - A Goo-like minion which is stuck on a wall that shoots at Bentley and takes away some health. Requires multiple hits to kill.
- Picking yellow power-ups will progress your upgrades by 1/5, picking 5 of it will increase your power level by 1.
- Picking red power-ups will regenerate your HP.
- Picking Core power-ups will increase your power level by 1.
- Taking damage will decrease your power level.
- When playing co-op, the players share a health bar.
- The music in this minigame is a remixed version of the music from Bentley Comes Through, a level from Sly Cooper and the Thievius Raccoonus.