Trophies that don't fit exactly into the story are listed here. Some are obtained through progression, whereas others will require more thought. None should be overly complicated, however.
The first trophies you should be aware of are for collecting all of the data clusters, which shouldn't be out of your way at all since you need a vast majority of them to purchase every power upgrade.
The most time-consuming trophies are these next two. You need to not only play for 40 hours, but you need to play at least two hours of both genders. This doesn't mean separate game saves; you can change your gender at Image as Designed.
Upgrading a weapon is important for finishing challenges, but you also want to fully upgrade a weapon to its full potential for a trophy. Melee weapons tend to have fewer upgrades than others. Customizing all of the weapons in your weapon radial is free and is also related to a trophy.
For this trophy, you need to prove your movement prowess by jumping from the roof of the 3 Count Casino (southwest) to the nuclear power plant (northwest) without touching the ground. Running on walls, landing on rooftops and other buildings, and flying in vehicles is allowed as long as the ground is your enemy. You can either do this the intended way by jumping from building to building (it isn't hard) or by calling in a flying vehicle of some kind after jumping from the 3 Count Casino. It'd be wise to upgrade your Jump and Sprint as much as you can before attempting this.
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