Jim is clearly acting as a police officer ("I am a cop"). Jim angrily quits in Batman 519 and reiterates his resignation in 520, after which he runs a fledgling mayoral campaign; even after he drops out of the race, it is not realistic for him to be acting in the capacity depicted in Chalice until after Contagion. Alfred returns in Batman 521, and appears in Chalice. In Chalice, Two-Face escapes his commitment hearing following a recent confrontation with Batman; that was probably meant to be the Two-Face story from Batman 527-528, but could also be Batman: Two-Face - Crime and Punishment, which is after Alfred's return but before the introduction of the new Batmobile in Batman 526... at any rate, the simplest, and most likely intended, placement of Chalice is between Contagion and Legacy.