The Commonwealth's boogeyman is the Institute. They're set up to be the main antagonist in Fallout 4, only for the main plot to be turned upside down once the player arrives at their underground lab.
One of the horrors committed by the Institute was the CPG Massacre. It happened long before Fallout 4, and despite Shaun's assurances that the Institute is working for the Commonwealth's best interests, it's difficult to believe considering what the shadow organisation has done to the wastelanders above.
The Commonwealth Provisional Government (or CPG) was a post-war entity conceived by the Minutemen. They gathered at the Castle representatives from the most important villages in the area. They conversed there, most likely on how to bring the Commonwealth's people together and make it a safer place to live. It's unclear who the representatives were, although one of them was said to be speaking on behalf of the Institute.
According to the game's stats, the CPG lasted four years. However, it does not appear that much progress was achieved in terms of cleaning up the Commonwealth. This was most likely due to internal strife and a general inability to achieve a consensus. The Institute had become tired of the squabbles at this point. Many within the organisation wished to break off any contact with the Commonwealth, according to a holotape recording made by one of the Director's staff.
Others, on the other hand, thought it was a mistake and that the Institute should not abandon the wastelanders. The same holotape reveals that the Institute already had a large army of synthesisers at this time, and the individual in the recording proposes employing them to "keep order," whatever that means.
Despite the unidentified staff's protests, the Institute retaliated with violence. The organisation sent a synth to the negotiations after the four-year milestone. The man was one of the later synth models, and as a result, he resembled a person. As a result, he was allowed to attend the conference, when he allegedly shot every CPG representative. Nick Valentine reveals this to the Sole Survivor during one of his early affinity discussions. "The Commonwealth Provisional Government was over before it even got off the ground," he argues, despite the fact that the talks had been going on for four years.
After a long time has passed, the player can speak with Shaun about the occurrence. The Sole Survivor will emphasise that the Commonwealth's people require the Institute's assistance, particularly given their superior technology. Shaun, on the other hand, will respond that the Institute tried to work with the wastelanders above but that "it was a disaster." Since then, the organisation has concentrated on looking after its own. Interestingly, despite the harm the Institute has caused, Shaun believes the Commonwealth has nothing to fear from them.
There aren't many dialogue lines or writings in the game that address the CPG Massacre. What the player can find, though, are contradicting pieces of the same puzzle. On the one hand, the anonymous Institute staff claims that talks lasted four years, with the Institute sending a representative to try to achieve an agreement with the Commonwealth's citizens. Nick, on the other hand, appears to be implying that the Institute shut down the CPG before the negotiations could even begin. This mismatch, on the other hand, could be the result of Nick hearing skewed tales of the CPG Massacre.
There's also Shaun's bizarre note about how the Commonwealth shouldn't be afraid of the Institute. It's hard to believe, given that an Institute synth was the one who put an end to the CPG, much alone all the kidnappings, assaults, and murders perpetrated by the rest of the synthesisers. Granted, the CPG Massacre appears to have occurred decades before the events of Fallout 4. As a result, it's not out of the question that it happened before Shaun was taken from Vault 111.
If this is the case, the Institute was almost certainly still led by a different person or group of persons. Perhaps the old leadership meant to assist the Commonwealth at first, but grew frustrated with the CPG's unwillingness to cooperate. As a result, one of their synth agents is ordered to kill them all. When Shaun rose to power, he was either unaware of the violence that occurred during the CPG incident, or he was aware of it but wanted to keep it hidden.
Still, this doesn't explain why the Institute ordered the CPG representatives to be slaughtered. One hypothesis is that the Institute was initially supportive of the CPG but later realised it constituted a risk to the institution. Perhaps the other representatives sought more transparency and access to their resources, which the Institute would not have approved. Alternatively, the Institute may have believed that the CPG would jeopardise their power over the wasteland, leading to the decision to shut it down.
Another idea is that the synth representative malfunctioned during the talks, which would explain why the massacre occurred. Given that the Institute's humanlike synthesisers were still relatively new creations at the time, it's not out of the realm of possibility. Furthermore, it has already occurred once, with the occurrence of the Broken Mask. If this is the fact, the Institute may have intended to assist the Commonwealth's citizens, but the wastelanders lost faith in them following the CPG Massacre.
While all of these explanations are plausible, there is no way to know which one is accurate. Because there is so little information in the game concerning the CPG Massacre, all players can do is try to piece it together on their own. But one thing is certain: the episode does not reflect well on the Institute.