Kerry: Putin wants to shore up Assad and Russia influence

'On the Record' Interview, Pt. 1: Russia's bomb strikes in Syria took the Obama administration off-guard. Before the attacks, Sec. of State John Kerry discussed the complicated interests the US, Putin and Assad have with the looming ISIS threat

This is a rush transcript from "On the Record," September 30, 2015. This copy may not be in its final form and may be updated.

GRETA VAN SUSTEREN, FOX NEWS HOST: Earlier, Secretary of State John Kerry went ON THE RECORD. Now, he is in New York City for the U.N. General Assembly. We spoke to Secretary Kerry just hours before Russia began their surprise air strikes in Syria.

Late yesterday, Secretary Kerry and I talked about Vladimir Putin and ISIS.

(BEGIN VIDEOTAPE)

VAN SUSTEREN: Mr. Secretary, nice to see you, sir.

KERRY: Happy to be here. Thank you.

VAN SUSTEREN: All right, what would you do about Assad?

KERRY: Well, we are going to work with our members of the coalition, the allies who are all combined in order to fight ISIL. And now, hopefully, be able to get Russia to join in the effort to fight ISIL. But also to be part of a political track because you have to do both at the same time in order to try to come to a political resolution with respect to the transition to a government of credibility and a government of capacity in Syria.

My hope is, judging on the meeting that we had yesterday with President Putin, I believe there is an opportunity to be able to do -- to go down that political track because President Putin accepted the idea of a dual track effort. And he indicated a willingness to try to work through a political transition. Now what that means for Assad yet is not yet finalized, not determined.

VAN SUSTEREN: Do you have the sense that President Putin wants President Assad to go?

KERRY: I think what he wants is a solution to the problem and he understands that Assad is a major blockade to do that. As he's turned around and said, you know, I'm going to kick him out? No, he hasn't said that yet. What he has said is he is prepared to have a political process. And the end result of that process is really up to the Syrian people.

So there may be a way through that threading of a needle to come to an understanding about where we are heading. If Assad insists on staying there Syria will be destroyed for the simple reason that the Jihadist, the extremists attracted to the fight will come in even greater numbers and you will never be able to make peace until you resolve the question of what is happening with respect to the political tract of Assad.

VAN SUSTEREN: Was there any indication that President Assad even wants to leave or is willing to leave?

KERRY: There are indications that he has said publicly if the Syrian people don't want me, then I'm prepared to go. He has also --

VAN SUSTEREN: Do you believe that? I mean, there is a lot of indication there is a civil war there.

KERRY: I don't believe what he says. One way out, or one way or the other, and I don't wait to hear what he says. What I do care about is what Russia and Iran and other countries are prepared to do in order to try to solve this problem.

VAN SUSTEREN (Voice-Over): But within hours of our interview in his hotel last night, breaking news, the real Russian plan becoming evident, now Russia is launching their own air strikes in Syria. The news surprising many people in the United States. And just hours ago, Secretary Kerry addressing the U.N. Security Council.

KERRY: My colleagues, the government of Russia has argued that we must support Assad in order to defeat ISIL. But the reality is that Assad has rarely chosen himself to fight ISIL.

VAN SUSTEREN: And while going ON THE RECORD yesterday, Secretary Kerry saying such an alliance will create problems in the fight against ISIS.

KERRY: Putin now has put himself in the center of a problem. He is there. He is on the ground now. He says he's going to be there to fight ISIL. Well, guess what?

If he is there to fight ISIL and he doesn't have the support of Sunni, he is never going to succeed in that fight. So he may wind up in a very serious situation. The only problem is it also means that Syria goes down hill.

So we all have a responsibility because of the numbers of refugees that are leaving the country, flooding Europe, changing the politics of Europe, an extraordinary process of destruction of historical sites and of people and the capacity of the country to be whole, that's what's happening because of ISIL's presence and because of Assad. So both problems have to be solved. And it may well be, you have to solve them simultaneously.

VAN SUSTEREN: What's in it for President Putin. I mean, he certainly has muscled his way and he's now got the security agreement with Iraq, Iran, Syria or the intelligence sharing. But what's in it for him? What's his interest in this?

(CROSSTALK)

KERRY: Let me just point out very quickly that Russia has been coordinating with Iraq and in the region for many years. This is not new. And the intelligence that they will be sharing, getting from the Iraqis we know is nothing that interferes with us or threatens us in any way, whatsoever. And if you are going to coordinate in an effort against ISIL, you are going to need some kind of coordination with respect to whose operating where and what they are going after.

So President Obama and President Putin agreed to immediately engage in military-to-military deconfliction at the most basic level, not yet to cooperate in the missions but to de-conflict.

VAN SUSTEREN (Voice-Over): But today's Russian air strikes, a clear violation of Russia's supposed commitment to de-conflict. But at the United Nations today, Secretary Kerry still pushing for deconfliction.

KERRY: We are prepared to welcome those efforts and to find a way to de-conflict our operations and thereby multiply the military pressure on ISIL and affiliated groups. But we must not and will not be confused in our fight against ISIL with support for Assad.

Moreover, we have also made clear that we would have grave concerns should Russia strike areas where ISIL and al Qaeda affiliated targets are not operating.

VAN SUSTEREN: But "Fox News" learning the target was not ISIS leading some people to believe the target may actually be Syrian rebels and part of a plan to prop up Syrian Dictator Bashar Assad.

KERRY: We will continue our missions exactly as we are doing. And today, the French have now joined in the fight with us, in our flying missions. Australians are coming in. There is a lot happening. And I am convinced over the course of the next days that there will be additional pressure on ISIL.

The problem is and remains as we keep telling Iran and Russia, if you do not find a way to be inclusive with respect to the Sunnis, 65 million of them, from Baghdad all the way up to the Turkish border, through Iraq and Syria, if they are not brought in to this fight, if they are not brought in to the governing, you cannot solve the problem of ISIL and you certainly can't solve the problem of Assad in Syria.

VAN SUSTEREN: OK. So what's in this for President Putin? What are his designs? I mean, he seems to be very busy.

KERRY: Putin has a very legitimate concern about 2,000 Chechens who are in Syria, learning how to fight and be terrorist and very threatened by surrounding countries from which there are even more people who are there to learn the fight.

I think he also is fearful that his client, Assad, was losing ground to both ISIL and the opposition. And, therefore, he wanted to shore him up. But I think shore him up with a view to trying to maintain Russia's influence and presence in the country even as they try to secure a political solution.

It's a complicated, very complicated series of different interests in relationships, all of which have to be managed in a way to try to secure a resolution and I think we will find out. But this is not going to happen in one day or, you know, one week. It will take a little while to sort through the modalities. And put the political tract together. And that's what we are going to do.

(END VIDEOTAPE)