Following the Fall of Beacon, General Ironwood contemplated his mistakes when his technology was hacked. Without Ozpin to guide him, James had to trust his own judgement on how to stop Salem, and decided to use a new approach to fight her.
With this in mind, Ironwood informed Penny and Winter , as well as the Ace-Ops, about Salem, planning to restore global communications by replacing the CCTS by using Amity Colosseum as a satellite and tell the world about Salem as well as to protect the Relics. Additionally, the group decided to make it so that Winter would replace Fria as the next Winter Maiden.
After the Ace-Ops team captured Team RWBY, Team JNPR, Qrow Branwen, and Oscar Pine in the city of Mantle, Ironwood apologized for the misunderstanding between the groups. He went on to explain to the group about his group's formation, under the belief they need to trust one another in other to defeat Salem, informing them of his plans.
Ironwood's Group was aware someone was staging fake Atlesian attacks over notable people who was against Ironwood in Mantle, including Forest. To combat this, James sent Clover Ebi to track down the killer who was behind this. They also sent Marrow Amin and Penny to Robyn Hill's election party in case something went awry. They later discovered Tyrian Callows was behind the massacre at the party. Due to the massacre, the Happy Huntresses began to block Mantle's resources from reaching Atlas, thus outright halting the Amity project. The group was later invited to a ball at the Schnee Manor by Jacques Schnee.
During the Battle of Mantle, Ironwood's Group participates in aiding against Salem's Forces and the Grimm in the city, with Clover aiding in the capture of Tyrian Callows alongside Robyn Hill and Qrow. Ironwood battles Arthur Watts in the Amity Communications Tower after revealing the existence of Salem to the world. Upon arriving in his office, Ironwood discovers an infiltrator had left a message to him that Salem had entered the Academy. He summons the Ace Ops and enters into conflict with Ruby's Group once they oppose his plan to abandon Mantle and save the city of Atlas.
Ironwood calls for the arrest of Ruby's Group, leaving for the Atlas Vault. The Ace Ops are defeated by Team RWBY, par Clover who is killed by Qrow and Tyrian elsewhere in the Solitas tundra after an escalation of an argument with Robyn Hill.
At the vault, Ironwood has an argument with Oscar Pine over his choice, leading to James shooting Oscar out of the vault and into a pit.
Following his discover of Cinder's chess piece, Ironwood sends Winter and Penny to claim the powers of the Winter Maiden from Fria. They are interrupted by Cinder, who had followed them into the Atlas Medical Facility. After a battle, Winter is nearly killed and Penny takes the powers for herself as Cinder flees upon seeing Ruby Rose'sSilver Eyes. Penny betrays Ironwood's Group, joining Teams RWBY and JNPR, and Winter reports to the general what happened.