Nothing is known about the submarine's history before the outbreak aside from the fact that the Weapons Officer was Riley.
At some point during the outbreak, an unknown event killed the crew and the submarine washed up on the shores of Galveston, Texas. Only two known members of the crew survived the event: the Weapons Officer Riley and a crewmember named Walter.
One of the keys to the submarine's nuclear missiles landed in the hands of Walter while the other landed in the hands of cult leader Theodore Maddox who saw the sub's missiles as a way to bring about the destruction that he felt humanity needed in order to get a new beginning. Twomembers of the cult hired bounty hunter Emile LaRoux to kill Walter and retrieve the second key for them.
The two men await Emile's arrival beside the sub with one spray painting "The End is The Beginning" on the sub's side. Emile is able to hunt down and kill Walter, but before he can make his rendezvous with the two men, Virginia hires him to hunt down and kill Morgan Jones. Morgan ultimately kills Emile in self-defense and takes the key for his own.
As the older man finishes up the spray paint, a walker approaches and he puts it down. The men become worried as Emile should've arrived by now, more walkers are bound to show up and they need the key. The two decide to wait for Emile in another location and leave the sub sitting on the beach.
On his way to Humbug's Gulch in search of Grace, Morgan is ambushed by the twomen who hired Emile to get the key from Walter. The men demand the key from Morgan and attack him, forcing Morgan to kill both men. Studying the key, Morgan is left wondering what it unlocks.
Riley and three cultists hunt Morgan and Grace for the key that is still in Morgan's possession, but he kills the three other cultists and forces Riley to flee. In Grace's dream, Athena is wearing the key which she states that Morgan gave to her as a reminder of "the price of peace." When Riley returns and demands the key at gunpoint, Grace has Morgan hand it over to him, convinced that Athena will bring everyone together based on her dream.
After Cole's Group is wiped out, Alicia asks how Teddy intends to bring about the destruction of everything. Feeling that Alicia has earned the truth, Teddy reveals that the keys go to the USS Pennsylvania washed up in Galveston. The keys, when used, will launch a nuclear missile from the sub which Teddy believes will be enough to do the job. Alarmed, Alicia takes Teddy's radio at gunpoint and she manages to contact Victor Strand. As more cultists arrive, Alicia asks if she can trust Strand and once he confirms that she can, Alicia warns him that she knows what the keys are for and that he must get to Morgan and they need to find a beached submarine near Galveston. Riley snatches the radio from Alicia before she can pass on anymore information and Dakota is sure that Strand will simply get as far away as he can rather than doing as Alicia wants.