

The new system allocates 6 slots to weapons, with each weapon taking up a varying number of slots based on the weapon's size. Shifter also contains a modified multiplayer game featuring additional selectable player models and a new inventory system. Also, Shifter adds a handful of customized weapons, a feature that gives skill points for kills (and a stealth bonus, if applicable, at the end of each level). This has been moved around since being brought back.

JC is supposed to overhear a conversation between Lebedev and Tracer Tong in which Tong is telling Lebedev to kill JC, but Lebedev is insisting that JC can be convinced to change sides. Another example is at the airfield's helicopter bay in one of the offices. This makes saving him worth it, but it doesn't actually happen, so in Shifter, it does. For one example, after rescuing Ford Schick from MJ12, he's supposed to appear in Smuggler's hideout - and he even gives you an augmentation upgrade canister. Shifter re-integrates a few features which were left out of the game, but were later found in the game's source code.
