[4] 1989, after working for Vintage Sports, Cone took over as the coach of the Alaska Air Force with players such as the famed Bruise Brothers duo of Yoyoy Villamin and Ricky Relosa, and Abet Guidaben.

The group's complaints stemmed from Article 40 of the Labor Code that only allows the hiring of a foreigner only after determining that no Philippine resident is competent, able, and willing to perform services at the time of application.

Cone was able to return to PBA coaching when he gained permanent resident status after his August 1991 marriage to Filipina girlfriend Cristina "Cris" Viaplana.

After several struggles, Cone's team would have a strong group of locals Lastimosa, Johnny Abarrientos, Bong Hawkins, Jeffrey Cariaso and Poch Juinio, while having import Sean Chambers for the Milkmen.

Duremdes, playing a limited role with the Pop Cola franchise, rose up to the occasion in 1998 under Cone's tutelage, winning the PBA Most Valuable Player Award at 24 years of age.

That year, Cone was hired as the coach of the Philippine Centennial Team led by Duremdes, Abarrientos, Lastimosa, three players on Cone's Alaska team, and PBA stars Alvin Patrimonio, Marlou Aquino, Vergel Meneses, Allan Caidic, with defensive anchor Andy Seigle and rising star Olsen Racela.

Cone, however, would lead the young team of John Arigo and Ali Peek to runner-up finishes in the 2002 Governors' and All-Filipino Cup.

A year later, the Aces added UAAP star Mike Cortez and Brandon Cablay, leading Alaska to the 2003 PBA Invitational Cup championship, Cone's 11th title.

However, a day later, the Aces' official website reported that Cone has agreed to a new deal to stay on as the team's head coach for the 2006–07 PBA season.

By winning the season-ending best-of-seven series 4–3, the former Purefoods ballclub won its second championship over the last five conferences and more importantly the 15th career title for Cone, putting the veteran coach in the company of the great Baby Dalupan at the top of the all-time list.

[13] In September 2019, he was appointed head coach of the national team again[14] for the 2019 Southeast Asian Games following the resignation of Yeng Guiao following the Philippine's poor performance in the 2019 FIBA Basketball World Cup.

[15] Cone was appointed to coach the national team for the 2023 Asian Games after Chot Reyes stepped down shortly following the 2023 FIBA Basketball World Cup.

[16][17] Despite taking over on short notice, Cone was able to lead the team to a gold medal finish in the continental competition, their first since the 1962 Asian Games.