Leonard James Akaar (Born in a TOS episode)
Laas (The Changeling)
Sirella (Martok's Widow)
Children of Canon Characters:
James O'Brien (Son of Smiley O'Brien and an unknown mother)
Joshua Riker (Son of Thomas and an unknown mother)
Akira Sulu (Grandon of Demora, Great-Grandson of Hikaru)
Cerin Teresa (Daughter of Dukat and Mika)
Characters from the Novels:
Characters whose current whereabouts are referenced in-game but who are NOT seen:
Kira Nerys - Kai of the Bajoran Religion
Leeta - First lady of Feringinar
Quark - Proud owner of his own moon, proprietor of Quark's Bar and Embassy in absentia
Thomas Riker - Deceased
Rom - Grand Nagus
Sela - Romulan Empress
Sisko - Inside the Bajoran Wormhole; it is indicated he speaks highly of you to the Prophets
Characters whose whereabouts are referenced in supplemental materials:
B-4 - Stored in a holodeck, indication he may be a hologram now.
Leah Brahms - First wife of Geordi LaForge, mother of his children
Beverly Crusher - Is (or was?) married to Jean-Luc Picard. Their son (artificially conceived?) lives on Mars. She commands the U.S.S. Pasteur (?).
Data - Captain of the Enterprise 1701-E
The Doctor (Joe?) - Campaigning for holographic rights
Dulmer - Aware of changes to the timeline, aware of both the Abramsverese and the novels.
Vic Fontaine - Holo-program still running, may have left DS9 by this point
Jack (Augment) - A respected professor who advocates NOT combatting the Undine.
Admiral Kathryn Janeway - Tactical expert on the Borg.
Geordi LaForge - Returned to Starfleet and commands the U.S.S. Challenger 71099. Divorced from Leah Brahms. Married to his Chief Engineer. On somewhat unfavorable terms with Data.
Lucsly - Active Field Agent in Temporal Investigations
Bruce Maddox - Saved B-4 from disassembly. Made breakthroughs in discovering the backup of Data but refused to overwite B-4 on ethical grounds, which Geordi ignored.
Jean-Luc Picard - Former ambassador to Vulcan, now retired in France. Is (or was?) married to Beverly Crusher.
Q - Posing as a mental institution orderly who observes and torments Dulmer.
William Riker - Married to Deanna Troi. Commands the Titan. Daughter Natasha lives on Mars.
Seven of Nine - Left Starfleet in disgust, believing they underestimated the Borg
Jake Sisko -Author on Anslem, famed journalist.
Deanna Troi - Married to William T. Riker
Nog - Chief Engineer of the USS Enterprise 1701-E
Just wanted to put in an update. When you are finishing up the badlands mission where you meet Joshua Riker, he wants to pass a message on to his Uncle Will, and Captain Kurland of DS9 says that he will send the message to Admiral Riker.
So, sounds like he's not retired yet. I assume as an Admiral, he would no longer be Captain of the Titan.
Sela shows up in the game, at least on a Romulan Scimitar Dreadnought you fight, and you see her picture while she gives a brief hail. An Iconian ship tows Romulan Empress Sela's ship I.R.W. Leahval to an unknown location, leaving the question of whether Sela was rescued or abducted.
The I.R.W. Leahval is a Romulan Scimitar Dreadnought and the flagship of the Romulan Star Empire.
So, hopefully everyone has been able to finish the last 2800 mission, Boldly they Rode.
The Enterprise-F makes an appearance, commanded by Captain Shon. (The Andorian captain who was in the Borg briefing with you at the start of the 2800 mission.)
No mention of the Enterprise-E. So I guess they are just going to leave that hanging and the E is just working (or lost) on it's Deep Space mission....
[In 2408 Starfleet loses contact with Star Base 236 and sends the U.S.S. Enterprise, commanded by Captain Data, to investigate.]