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- For the player's own lair, see Base.
Secret Bases are the final areas of a series of missions. Usually indoors, these locations are sometimes used for Duos.
Levels shown below are the approximate level your character will be when entering the base, if following your mentor's storyline from the beginning.
Joker's Storyline Edit
- Gotham Warehouse (lvl 3)- Huntress, assist by Catwoman
- Distribution Centre - Supplier Diego, assist by Killer Croc
- Cape Carmine Lighthouse - Bane, assist by Killer Croc
- Joker's Funhouse - Robin, Free Harley Quinn
- GCPD Special Crimes Unit (lvl 15)- Free Clayface
- East End Regal Hotel (lvl 15)- Batman, Joker helps out
- WayneTech Storage Facility - appearance by Mr Freeze
- Gotham Mercy General Hospital - Mr Freeze
- Intergang Penthouse -
- Mysterious Warehouse - Kyle Abbott and Whisper A'Daire, Batwoman captured
- Temple of Crime - Bruno Mannheim, assist by Deathstroke
- OMAC Base - Brother Eye, Killer Frost helps out
- T.O. Morrow's Hideout (lvl 30)- Red Tornado and Batman,Joker helps out, T. O. Morrow escapes, Harley Quinn and Robin are sick by toxin
- Gotham S.T.A.R. Labs (lvl 30)
- S.T.A.R. Labs Space Station (lvl 30)- Robotic Batman and Robotic Joker
- Arkham Asylum (lvl 30)- Defeat Robotic Joker, Decide Joker's Fate
- Sentinels of Magic Base (Chinatown) (lvl 3)-Re direct the portals to Hades feat is here
- Sentinels of Magic Citadel (lvl 3)- Doctor Fate, assist by Brother Blood
- MPD 8th Precinct Metropolis Science Police HQ - Cyborg, Starfire, Nightwing, Donna Troy, and Raven
- New Troy Central Station - Wondergirl, assist by Giganta
- Chinatown Electronics (lvl 15)-
- Chinatown Cafe (lvl 15)- Wonder Woman, assist by Circe
- Sentinels of Magic Base (Midtown) - Zatanna and Etrigan, assist by Eclipso
- A Shadow of Hell - Cyborg, Starfire, Nightwing, Donna Troy, Beast Boy and Raven, appearance by Brother Blood
- University Warehouse -
- Gotham University - Isis, appearance by Black Adam and Felix Faust
- C.A.O. Dam (lvl 30)- Last Guardian of Limbo, assist by Brother Blood
- Limbo (lvl 30)- Last Guardian of Limbo, assist by Brother Blood
- Oblivion Bar (lvl 30)- appearance by Doctor Fate, Brother Blood, Etrigan, Cheetah, Donna Troy, Wonder Girl, Captain Marvel, and Solomon Grundy.
- Shadowlands (lvl 30)- Wonder Woman and the Shadow Keeper, assist by Circe
Lex Luthor's Storyline Edit
- Metropolis University (lvl 3)- Power Girl, assist by Parasite
- HIVE Base - Queen Bee
- Metropolis General Hospital - Supergirl, appearance by Doctor Psycho
- S.T.A.R. Labs Research Facility (lvl 15)- Steel
- S.T.A.R. Labs Facility (lvl 15)- Superman, assist by Lex Luthor
- Old S.T.A.R. Labs - the Flash (Barry Allen) and the Flash (Jay Garrick), assist by Gorilla Grodd
- Metropolis City Hall - Green Lantern (John Stewart), assist by Sinestro
- JSA Safehouse - Wildcat
- JSA Metropolis Wing - Hawkman, Hawkgirl and Green Lantern (Alan Scott), Free Sinestro
- Daily Planet Building (lvl 30)-
- Watchtower (Instance) (lvl 30)- Superman, assist by Lex Luthor