There are two types of rewards available in Survival Mode: clear rewards and drop rewards. You may be rewarded with more Cores than you would receive in Autoplay Mode if you manage to survive to the end. On the other hand, the more Cores that are acquired, the more Corrupted Mercs become, and Mercs who reach the maximum Corruption level can no longer be deployed.

Clear Rewards

When you defeat a stage’s boss and succesfully survive, you will earn Cores.

Drop Rewards

After defeat the Infected and bosses may drop Cores and Crystallized Mercs.
Note, however, that if your Stamina reaches zero, you will lose the rewards you have earned by playing up to that point.