Arkham Asylum Incident
In the sewers under the asylum, Batman searches for the plant spores in Croc's lair to synthesize the antidote. It consisted of mostly tunnels and maintenance platforms and several locked gates.
Arkham City Incident
Killer Croc had a small hideout on the sewers under Arkham City. It included a small matress, a table and
several skulls. Scanning this location was required to solve a riddle. In addition, when returning to the surface after meeting Ra's Al Ghul, one can see a cameo appearance by returning via the sewers and throwing a remote batarang to a hidden button. Both of these unlock Croc's Character bio.
After Arkham City incident
After the closing of Arkham City, Croc was hired by Harley Quinn to protect the antidote to the Joker toxin, When Batman came into the sewers with Gordon and Aaron Cash to get the antidote he ambushed all three but was defeated by Batman using his last Freeze blast. After this it's unknown where he went to before The Arkham Knight incident.
Before Arkham Knight Incident
Killer Croc had been hiding inside a lighthouse located near Ace chemicals, as evidenced by a large pile of bones. Scanning this pile is required to solve a riddle. The picture shown on the Gotham City story also has raw meat hanging from the ceiling.
Arkham Knight Incident
On Halloween night Killer Croc had crashed the Iron Heights Penitentiary airship and used it as a base when he took the Warden hostage.