In 'The Candidate', Sayid (Naveen Andrews), Jin (Daniel Dae Kim) and Sun (Yunjin Kim) were all killed when a bomb planted by the Man In Black exploded.
Asked why the characters died, Lindelof told Entertainment Weekly: "Because now you know this show is willing and capable of killing anyone."
Cuse added: "There is no ambiguity. [The Man In Black] is evil and he has to be stopped... When we watched the death scenes ourselves, it was brutal. [But] the story always comes first."
The duo explained that it was important that the characters were killed to establish that Fake Locke is evil.
"In many ways, the season was structured as a long con on behalf of the Man In Black," Lindelof said. "Once we revealed that Locke was the Monster, we knew the audience would immediately mistrust him, and we would have to spend at least a dozen episodes of Locke trying to convince the audience that he did not have malevolent intention, that all he wanted to do was get off the Island.
"But everything he was doing was leading up to one moment, which was [trying to] get the candidates in one fell swoop. He knew if he just killed one of them, everyone would know what he was up to."
Cuse went on: "There will be very little debate at the end of this episode that [Fake Locke] is evil and bad and has to be stopped. The main narrative reason for him killing our main characters is to establish how much of a bad guy he is and to clearly identify him as the antagonist rolling into the end of the series."
Lost continues Tuesday at 9/8c on ABC in the US and Friday at 9pm on Sky1 in the UK.