Can't remember where I read this years ago, or where it came from, a video game or a comic book or whatever... but supposedly it's canon... take it with however many grains of salt you wish.
Seraph is from an early version of the Matrix where instead of Agents, there were Angels who kept kept watch over the humans. Probably the "paradise" version of the Matrix i.e. the origin of the whole 'Book of Genesis' motif. When that version was decommissioned, naturally all of the Angel programs were to be deleted, but Seraph went rogue and ended up being one of the first to join the Merovingian and work for him. Eventually Seraph betrayed Merv, and Merv's punishment was to take away his angel wings. This is why Merovingian's men refer to him as "Wingless" and Merv himself greets him in French with something like "Ah, it's the angel without wings."
Anyway, as a rogue program in the Matrix, the Agents were out to delete him every chance they got, hence Seraph's prior clash with Smith.
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