To their absolute shock, Flynn does not travel back to cause the crash; he actually the airship from its original landing explosion. The team quickly deduces his real, more sinister plan: Flynn intends to let high-profile dignitaries and historical figures board the ship for its return flight to Europe, and then detonate it over the Atlantic. This would effectively erase several people vital to the future formation of the United Nations.
The pilot successfully plants several long-term narrative seeds to hook the audience: Timeless 1x1
Flynn reveals a journal to Lucy written in her own handwriting, claiming she gives it to him in the future to help him on his mission. To their absolute shock, Flynn does not travel