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Proto weapons were special versions of Agency's weapons that could be bought from the Agency vendor after upgrading the weapons to V4. The Proto weapons were only available in challenge mode. Proto weapons could be upgraded V4.
- Proto Hellfire Haversack
- Proto Wrist Mortar
- Proto Hardlight Fist
- Proto Kudzu Tangle
- Proto Whirlwind Throwtie
- Proto Lightning Rod
- Secret Agent Clank (first appearance)