The shadowed holographic man is Noye, a 25th century Krenim scientist and member of the anti-Iconian alliance. After he finds out that the alliance's actions erased his Tuterian wife from history, he embarks on an anti-Temporal Accords / anti-Federation campaign, founding the Temporal Liberation Front. Noye recruits Boratus the Vorgon (after Ajur is killed in a fight with the player), the Na'Kuhl (whose home star the Federation failed to save from the Tholians' stolen Tox Uthat), the Tuterians-turned-Sphere Builders, and Captain Leeta of the revived Terran Empire (turns out that Noye instigated the interphase event that sent the Defiant over to the mirror universe).
This story arc culminates with the player and their time police allies confronting the Temporal Liberation Front at Procyon V in the 26th century, as seen in "Azati Prime". The player character installs the Tox Uthat aboard the Enterprise-J to destroy all the spheres and neutralize the expanse.
Except that as we saw in the Enterprise TV series, Future Guy dispatched the Suliban to help pre-Federation Earth stop the Sphere Builders and the Na'Kuhl.