I think rat's story is obvious now.
-Between the crew disbanding and roger's execution he got approached by the cp9 or cp0
-rat dad asked the lorosei to spare him and they accepted by respect for his heroic actions during god valley (killing boogy's dad)
-rat accepted to work for the WG in exchange for them to spare the remnants of the roger's pirates, they accepted again
-The roger's pirates somehow learned this and decided to make a vow of silence to not endanger the rat's life
-rat is an undercover WG asset who's work is to kill the problematic pirates or at least not letting them getting stronger, his target was were shiki, mihawk, Kidd etc.
-he is secretly doing is own things behind their backs
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You can't have it both