The Chronolog Scanner Array is located within the Temporal Security Annex and monitors history for illicit time jumps and temporal distortions. They are monitored at all times by a member of the Temporal Protectorate
They function in limited sensitivity to give them the speed necessary for continuous monitoring. As in automatic mode they aren't able to detect minor distotions, thorough manual scans are performed twice a year.
Agent 3 sabotaged the Chronolog Scanner Array security grid by crossing a couple of the feedback jumpers, and entered unnoticed the Pegasus Warehouse, there shadowing Gage Blackwood's time jumps to fool the scanners.
Agent 2 ran an unscheduled manual historical scan[1], and discovered temporal ripples indicating that someone had gone back to that time and affected a historically important object or event. He soon found that they exactly coincided with several of agent 5's research mission dates.
Commenting on this, William Daughton testified that the scanners were performing properly, and at no point during the period in question was an unsanctioned time-jump detected - a fact corroborated by the security logs. However he expressed the possibility that someone could have shadowed Agent 5's jumps within a few seconds to the same location; in such case, the Chronolog Scanners wouldn't recognise it as a second jump.
Notes[]
It's possible that the Chronolog Scanners also appear in the first game, monitored by the player when Elliot Sinclair's is detected, although they aren't mentioned as such in dialogue.