Milligan's next work for 2000 AD was Bad Company, with Brett Ewins and Brendan McCarthy. It can be thought of as a much bleaker version of Sooner or Later, this time holding a dark mirror up to the Britain of the first and second world wars rather than that of Thatcher. Aged 24, rookie soldier Danny Franks is marooned on the alien planet of Ararat, fighting a hopeless war with a group of mentally-disturbed misfits almost as dangerous as the sadistic extra-terrestrials on the other side. There is still word-play (the well-educated Danny, whose father was an academic interested in the history of words, narrates the first story in his war diary), but the humour is that of the gallows rather than the dole queue.
A prolific author apparently sharing the tenacity of Danny Franks (Danny won't stop writing even if grotesque alien monsters are trying to kill him), Milligan wrote many more strips for 2000 AD. These included The Dead (in which a likeable oddball tries to salvage something from a nightmare landscape... again); Freaks; Judge Planet; Tribal Memories; Bix Barton; Hewligan's Haircut; Shadows and Counterfeit Girl. He has also written Judge Dredd stories.
Milligan has worked for other British publishers including Titan Comics, and also for DC (on titles such as Skreemer with Brett Ewins and Steve Dillon, as well as Batman), Vertigo (on titles including Shade the Changing Man, Enigma, Egypt, The Extremist and Animal Man) and Marvel (on Elektra). He and Brendan McCarthy wrote a strip called Skin, about a young man with congenital defects caused by thalidomide, which was considered so controversial and explicit that Crisis refused to print it. It was eventually released as a graphic novel by an American publisher without causing any major civil unrest. Oh, and he wrote some scripts for M.A.S.K.