The score from each stage in the Alliance Operations is defined by the enemies defeated, speed of completion, and the amount of Hero health left at the end of a stage. Big combos and great matches are also taken into account. Using Continues has a negative effect on the stage score. The results screen at the end of a Stage shows the factors affecting the score in more detail.
The Alliance Ops has two separate scores:
Alliance Score: The total score of your entire Alliance
Personal Score: Your total contribution to the overall Alliance score
Players will receive rewards based on their overall Alliance's overall rankings as well as their overall ranking as individual players. Players can see examples of possible loot along with more information by clicking on the Rewards Tab in the Alliance Operation View and on the tooltips for the leaderboards.