Crosscurrent

Crosscurrent is a Star Wars Expanded Universe novel by Paul S. Kemp focusing on Jedi Knight Jaden Korr six months after Legacy of the Force, and Jedi Master Relin Druur as he is flung 5000 years into the future aboard a ship full of Sith. It's sequel Riptide was released in late 2011.

Tropes used in Crosscurrent include:

Apocalyptic Log: Jaden and Kheydan find some of the last logs of the Imperial scientists in the abandoned cloning facility.
Anti-Hero: Assailed by self-doubt and uncertainty, Jaden is solidly a Type I. Relin gradually slides into Type IV by the end.
Anyone Can Die: Even the main character...
Arc Words: "There be dragons."
Back from the Dead: After Korr is killed by a clone of himself by having his memories (and perhaps also his consciousness) pulled into a Rakatan device, his apprentice brings him back by subduing the clone and using the device on him, transferring Jaden into his body.
Bloody Handprint
Clone Degeneration: The escaped clones suffer from a horrific disease/syndrome caused by them being clones. Even the children of two clones suffer from it. The only one immune is Soldier and possibly the Iteration.
Clones Are People, Too: In the second novel, the clones of Mara, Lumiya, Kyle Katarn and even Jaden himself that escaped from the facility in the first novel have their own personalities that are different than their base. Most of them are completely mad and sick from some sort of disease, though.
Clone Degeneration
Cloning Gambit: Unintentionally on the part of Jaden.
Cool Ship: The Junker and Kell Douro's Predator.
Cloning Blues
Darker and Edgier: It's no Death Troopers, but it's definitely more gruesome than the average Star Wars book.
Determinator: Early on Relin is subjected to a maiming from Saes' lightsaber, numerous minor injuries, radiation poisoning that is slowly killing him throughout the book, and emotional trauma that eventually causes him to slide into the dark side, but he refuses to give up on his mission to destroy the Harbinger.
Distress Call: Jaden thinks one is coming from the Imperial facility. It's actually a warning to stay away.
Expendable Clone: Played somewhat straight with the Iteration, who was never allowed to have a personality of his own and implanted with an earlier version of Jaden Korr's memories and then with Korr's own personality
Fat Bastard: Reegas Vance.
Fallen Hero: Saes Rrogon, Relin Drurr.
Fingore: Jaden looses three of his fingers while dueling an insane Jedi clone.
Good with Numbers: Marr Idi-Shael, who is capable of calculating perfect hyperspace jumps with minimal aid form the nav-computer.
Gone Horribly Right: The old Imperial experiment to create Force-sensitive clones by combining the DNA of various Jedi and Sith. Suffice to say that the result involved gratuitous amounts of human sacrifice and cannibalism.
Heel Face Turn: Soldier at the end of the second novel.
Here There Be Dragons: Jaden Korr uses "There be Dragons...”, when thinking about his doubts about himself, the force, and everything.
Heroic Sacrifice: Drev Hassin, Relin Druur.
In Medias Res: The second novel opens with a scene from the last portion of the book, the majority of which is a flashback to how they got in that situation.
Me's a Crowd: At one point toward the end of Riptide, there are three versions of Jaden Korr in the same area: the dead body of Korr himself, Soldier, and the Iteration that killed Korr.
No Such Thing as Space Jesus: Mother, whom the majority of the escaped clones worship, turns out to be a sentient Rakatan space station who has gone partially mad from the isolation of space. She absorbs the head of her cult amongst the clones and rampages through the station before being killed.
Thrown Out the Airlock: Nearly happens to Kheydan in the second book at the hands of the clones. When they state their intentions of executing him, he actually demands that they kill him this way (rather than with a lightsaber).
Time Travel: The Harbringer travels 5,000 years into the future, leaving both the Sith crew and lone Jedi Master aboard as Fish Out of Temporal Water.
Tomato in the Mirror: Throughout the second novel, Korr is shocked to see a clone of himself (Soldier) amongst the escaped clones from the first book. He wonders if he actually is a clone. Happens later when the resurrected Jaden cleans himself up at the end of the book and finds that a childhood scar has disappeared.
Vomit Indiscretion Shot: There is a surprising number of instances of puking.
You Cloned Hitler!: The second novel reveals that one of the escaped clones from the first book is a clone of Lumiya, a Sith who was a secondary villain in the Legacy of the Force series.
Your Head Asplode: Kell suffers this from a blaster shot at point-blank range.
What You Are in the Dark: Kheydan Faal is attacked by Kell Douro and left badly injured but not killed as a message to turn back, leave the facility, and not come back for Jaden. Kheydan knows he could just leave and save himself, but decides to finally take a stand and stop running, and follows after Kell to save Jaden.