The Justice League and Watchtower
7 episodes of Smallville carry this thread, 6h 43m in all — 4 of them are in The Essentials.
Arc membership is derived from each episode's own summary text, gated to the seasons the sources place each arc in. It shows where a thread is foregrounded, not every episode it touches.
In airing order
The Green Arrow, Impulse, Aquaman and Cyborg try to destroy LuthorCorp's secret laboratory, but Impulse is captured and tortured by Lex, prompting the others to join forces as a team to rescue him.
In the eighth-season opener, the Justice League searches for Clark, but is stymied by the new CEO of Luthorcorp, Tess Mercer; and Chloe is held prisoner by a group who have discovered her powers, while Clark has been stripped of his by Jor-El.
Unable to control Davis, Chloe asks Clark to kill him. Seizing the opportunity, Tess gathers Plastique and a crew of meteor freaks to track down Davis, all the while planning a double cross. Things go awry, however, when Tess' true plans are discovered.
Clark and Chloe discover that someone is stalking and killing former criminals. Further research uncovers that the "criminals" are heroes of the last generation, framed by the government for crimes they didn't commit. Now new heroes must band with the old heroes--the Justice Society of America--if they hope to stop the killer.
Tess kidnaps the Green Arrow and leaves him in the hands of Amanda Waller, but he escapes with his secret identity intact. Oliver, Clark and Chloe return to the scene to investigate the kidnapping and find John Jones doing the same. Later, Waller threatens Chloe's life to get information on the Justice League.
Chloe becomes trapped inside Watchtower with Tess and tries to stop the Kandorians from accessing information on Watchtower's servers. Meanwhile, Clark learns that Zod's soldiers have superpowers, and a confrontation with Zod leaves Oliver near death and branded with a Z.
In the Season 9 finale, Zod claims to be the Blur and asks Lois to steal the Book of Rao from Clark; Lois asks Clark for full disclosure, but he refuses; Oliver disappears while he and Chloe attempt to fight the Kandorians by reconnecting Watchtower's satellites; Tess is seriously injured after confronting Zod; and Clark and Zod have a showdown as they battle for Earth.