Specifically, Kelly outlined the danger posed by homegrown terrorists and foreign fighters from around the world who have traveled to Syria and Iraq with plans to return home.
"The threat to our nation and our American way of life has not diminished," Kelly said during a speech at George Washington University. "In fact, the threat has metastasized and decentralized, and the risk is as threatening today as it was that September morning almost 16 years ago."
According to Kelly, the FBI currently has open terrorism investigations in all 50 states, and since 2013, there have been 37 ISIS-linked plots to attack the US.
Law enforcement agencies have investigated 36 cases of homegrown terrorism over the last 12 months, illustrating what Kelly called an "unprecedented spike" in a type of violence that is "notoriously difficult to predict and control."
And the Internet is playing a major role in fueling this homegrown violence, he said, pointing to cellphones as a tool used by jihadists to spread their message and provide "how-to" manuals for building explosives.
"If you are a terrorist with an Internet connection, like the one on your ever-present cellphone, you can recruit new soldiers, plan attacks and upload a video calling for jihad with just a few clicks," Kelly said. "And thanks to new and ever improving and proliferating encryption and secure communication techniques, it'll be a lot harder to find you and stop you before you take innocent lives."
While the US-led coalition has seen "wins" against ISIS and other radical groups on the battlefield in Iraq and Syria, "the expectation is that many of these 'holy warriors' will survive, departing for their home countries to wreak murderous havoc," he said.
Fighters from Asia and Europe, who have been trained by ISIS or other radical groups to make improvised explosive devices and acquired experience on the battlefield, are bringing those skills home.
Kelly's comments echoed those made last month by FBI director James Comey, who warned of a wave of ISIS fighters coming out of a "crushed" Islamic State, and called Western Europe "the front line of the FBI's and our US government's efforts to stop those killers."
"The future we worry about every single day is how do we spot and stop them as they flow out, bent on continuing the global jihad by taking the fight to innocent people?" he said.
Kelly also praised President Donald Trump's decision to carry out a strike against an Assad-regime airbase in Syria, last week, and talked about what took place in the Situation Room.
"I was involved in all of the discussions in the situation room with the President and he was very open to anyone at the table talking, giving their ideas," Kelly said.
"There was give and take, and he took all of that in and made in my opinion -- I don't think he'd mind my saying this -- made exactly the right decision."