He served as chairman of the Atlantic Council from June 2007 to January 2009, when he assumed the post of National Security Advisor which he held until resigning in November 2010.

[7] Returning to the United States in December 1968, Jones was assigned to Marine Corps Base Camp Pendleton, California, where he served as a company commander until May 1970.

He then received orders to Marine Barracks, Washington, D.C., for duties as a company commander, serving in this assignment until July 1973.

Remaining in Washington, his next assignment was as the Marine Corps liaison officer to the United States Senate, where he served until July 1984.

Jones was assigned to duties as deputy director, J-3, United States European Command in Stuttgart, Germany, on July 15, 1992.

During this tour of duty, he was reassigned as chief of staff, Joint Task Force Provide Promise, for operations in Bosnia and Herzegovina and North Macedonia.

Jones relinquished command as SACEUR on December 7, 2006, and was succeeded by United States Army General John Craddock.

[11] Jones' personal decorations include (foreign and non-U.S. personal and unit decorations are in order of precedence based on military guidelines and award date): The President of the United States of America takes pleasure in presenting the Silver Star to First Lieutenant James Logan Jones, Jr. (MCSN: 0-102030), United States Marine Corps Reserve, for conspicuous gallantry and intrepidity in action while serving as Commanding Officer of Company F, Second Battalion, Third Marines, THIRD Marine Division, in connection with operations against the enemy in the Republic of Vietnam.

On the night of 27 May 1968, while occupying a defensive position near Khe Sanh, Company F, came under heavy attack by a numerically superior North Vietnamese Army force.

Realizing the seriousness of the situation, First Lieutenant Jones unhesitatingly exposed himself to intense fire and fearlessly maneuvered across the fire-swept terrain while rapidly readjusting his defensive lines.

Ignoring the enemy rockets and hand grenades impacting around him, he boldly directed supporting artillery fire on his position to halt the hostile force's attack.

Continuing his determined efforts, he directed the delivery of accurate suppressive fire which repulsed numerous enemy attacks during the remainder of the night.

His heroic actions and outstanding leadership inspired all who served with him and were instrumental in his unit accounting for 230 North Vietnamese soldiers confirmed killed.

By his courage, aggressive fighting spirit and unwavering devotion to duty in the face of great personal danger, First Lieutenant Jones upheld the highest traditions of the Marine Corps and of the United States Naval Service.

[19] Following his retirement from the military, Jones became president of the Institute for 21st Century Energy,[20] an affiliate of the US Chamber of Commerce;[20] he also served as chair of the board of directors of the Atlantic Council of the United States from June 2007[21] until January 2009, when he assumed the post of National Security Advisor.

[24][25] Jones was also a member of the board of directors of Cross Match Technologies, a privately held biometric solutions company, from October 2007 to January 2009.

[26][27] Jones was employed on the board of trustees of the Center for Strategic and International Studies (CSIS), a bipartisan think-tank, from 2007 to 2008, and then began serving again in 2011.

[39][40] Jones serves as a Senior Fellow at the Bipartisan Policy Center (BPC), where he works on a variety of national security and energy-related issues.

Jones is an Advisory Board Member of Spirit of America, a 501(c)(3) organization that supports the safety and success of Americans serving abroad and the local people and partners they seek to help.

[45] Crowley speculated that Jones' record suggests he is "someone who, unencumbered by strong ideological leanings, can evaluate ideas dispassionately whether they come from left or right", and, "This is probably why Obama picked him".

[49] Jones was also responsible for convincing country music artist Toby Keith that he should record and publish his popular concert hit "Courtesy of the Red, White, & Blue (The Angry American)".