After Nix gives Cole the second Blast Core, Cole returns to Zeke's roof. Admiring how much the roof looked "just like home" Cole is surprised to see Zeke dress as a member of the Militia. Zeke claims that he's "Zeke Dunbar, Double Agent" a spy, but Cole asks which side he's spying for and recounts that his "faiths been shaken before". Whilst Zeke bemoans what he though was "water under the bridge", Cole retrieves the blast core from his bag, and after warning Zeke that he "Better not wake up in a Militia cage" activates the core.
Later, when Cole wakes, Zeke, now in his normal clothes, races up to tell him how some "idiots" are in the square below shooting anything that moves. Leaping down from the roof Cole makes his way to the park and takes on the Militia members. Once all three are defeated, Zeke calls Cole, mentioning the "weird glow" surrounding one of the fallen Militia members. Cole explains that he can feel it, that it's Ray Field Energy. Absorbing the ionic charge Cole launches an Ionic Vortex, a electrical tornado that leaves a trail of destruction in its path. Zeke contacts Cole and mentions that the Militia must have been around during Ray Sphere testing and how Cole needs to get some more of "whatever that guy had on him".
After this mission, Cole can now collect Ionic Charges for his Ionic powers.
This is the first and only mission to show Zeke in his Militia garb.
When Cole doubts Zeke's motives he is referencing Zeke's betrayal in Empire City.