Season 2:  The Coming of Shadows 

Episode 23:  "Points of Departure"

Captain John Sheridan is assigned to replace Jeffrey Sinclair as Commander of Babylon 5. As his first crisis to solve Sheridan is to coordinate with the Minbari government in an effort to hunt and capture a renegade Minbari warship the Trigati. Unwilling to accept the Minbari surrender to Earth ten years earlier they are determined to sacrifice themselves in order to destroy the only Earth captain to defeat a Minbari warship during the war - Captain John Sheridan, known to them as Sheridan the Star Killer. While Delenn is still in a cocoon, Lennier reveals the secret of why the Minbari surrendered to Earth ten years earlier even though Earth was outmatched.

Episode 24:  "Revelations"

G'Kar goes to Quadrant 37 to find out how their outpost was destroyed so easily and discovers that a very old and ancient enemy has returned. Unable to heal Garibaldi's injuries Dr. Franklin resorts to using an alien device designed for transferring the life energy of one person to another. Garibaldi comes out of his coma and with the help of telepath Talia Winters learns it was one of his own men who tried to kill him. Delenn's transformation is complete, she is now half Minbari and half Human.

Episode 25: "The Geometry of Shadows''

Londo has received help from Mr. Mordan twice now and has attracted the attention of the Centauri Royal Court. Lord Refa, a centauri of one of the royal families, visits Londo and confides in him his plans to dethrone the Emperor if they can count on Mollari's "associates". A rare group of Technomages, (magicians who use science to create the illusion of magic), assemble at Babylon 5 before departing beyond the rim of the galaxy. Sheridan promotes Ivanova and assigns her a diplomatic problem to resolve, to stop the Drazi from killing each other over the wearing of green and purple sashes. Before they depart one of the technomages warns Londo that he has been touched by darkness.

Episode 26:  "A Distant Star"

Commander Sheridan gets a visit from an old friend, a former captain of his that reminds Sheridan how much he misses commanding a star ship. Regrets of being assigned to a "desk" job leaves Sheridan questioning is purpose at Babylon 5. During a rescue mission of a ship lost in hyper-space, crew members encounter dark forces moving about the galaxy. The Minbari population at Babylon 5 object to Delenn representing Minbar now that she is only half Minbari.

Episode 27:  "The Long Dark"

Babylon 5 receives a signal from deep space coming from a ship lost for a hundred years with its crew still under cryogenic suspension. All of the crew except one is dead, killed by an unknown being who feeds off of its hosts. A raving lunatic from down below recognizes the creature, having been victimized by it in the past and tries to warn Babylon 5. Now that it is aboard Babylon 5 the creature starts killing and feeding off the inhabitants. The creature is known to some of the aliens aboard Babylon 5, known to them as a soldier-of-darkness from the past.

Episode 28:  "A Spider in the Web"

A peace keeper arrives at Babylon 5 determined to pass his proposal to end the Mars riots and mend ties with Earth. He is soon after murdered by an assassin who Talia Winters senses has already died. Identified as a member of the elite resistance group called "free Mars" his actions on Babylon 5 threatens the negotiations between Earth and Mars. Commander Sheridan learns the assassin has been a victim himself of a secret project called "Lazarus". Subjects on the verge of death were implanted with cyber intelligence and programmed to be "cyber zombies" to be used as secret operatives.

Episode 29:  "Soul Mates"

Londo's three wives arrive on the station. The Emperor has granted Londo the permission to divorce two of his wives and he must select which one is to remain his wife in title only. Londo enjoys the bitter rivalry that ensues between them. Talia Winters' ex-husband comes to Babylon 5 and he seems to have an unnatural ability of persuasion. Garibaldi is asked by Talia Winters to investigate him, as he is the only person to ever leave the Psi Corp. Her ex-husband convinces Talia he knows how she to can be free of the Psi Corp and she agrees to leave Babylon 5 with him.

Episode 30:  "A Race Through Dark Places"

Psi cop Bester learns of an organization that has been helping rogue telepaths escape the Psi Corp and that it is headquartered at Babylon 5. Garibaldi investigates who in the command staff has been helping the telepaths. The rogue telepaths on Babylon 5 kidnap Talia Winters and try to persuade her to join their cause. They demand a meeting with Commander Sheridan to explain their situation. The leader of the rogue telepaths recognizes that Talia Winters can help them deceive Bester, that she is more than she appears, the result of having been altered by Ironheart in the season 1 episode "Mind War". Delenn asks Commander Sheridan to help her understand what it is to be human and the two begin seeing each other socially.

Episode 31:  "The Coming of Shadows"

The Emperor of Centauri Prime visits Babylon 5 in an ill-fated attempt to heal old wounds between the Centauri and Narns. G'Kar sees this as an opportunity to assassinate the Emperor. Londo's associate from Centauri Prime, Lord Refa, arranges for Londo to meet the Emperor and give a speech that will further elevate their positions and plans to dethrone the Emperor. While on Babylon 5 the Emperor dies of a heart attack. Londo's associate, Lord Refa, sees this as an opportunity and Londo provides an example of their power by asking Mr. Mordan to destroy a Narn colony. In response the Narns declare war against the Centauri. Garibaldi learns of the Rangers under the leadership of Jeffrey Sinclair.

Episode 32:  "GROPOS"

General Franklin, Dr. Franklin's father, arrives at Babylon 5 bringing with him 25,000 "ground pounders" (ground troops) for a secret battle. With them they also bring a new and improved heavy weapons grid upgrade for Babylon 5. General Franklin's presence on the station disturbs Dr. Franklin as old differences between father and son flare up. The ground pounders suspect many of them will not survive the mission ahead of them and so try to get as much living in as is possible while at Babylon 5.

Episode 33:  "All Alone in the Night"

Delenn is called back to Minbar by the Grey Council who are concerned about her role now that she is only half Minbari. Fearing she has become alien to them they remove her from the Grey Council. Stripped of her title "Satai", she is allowed to continue as ambassador at Babylon 5. Commander Sheridan takes a fighter squad to investigate the disappearances of several ships in a nearby sector and is abducted by a race called the Stribe. They torture him and subject him to experiments in an attempt to investigate potential alien threats to their civilization. General Hague visits Sheridan and informs him there are unknown forces pulling the strings back home on Earth.

Episode 34:  "Acts of Sacrifice"

The war between the Narns and the Centauri heats up. The Narns are clearly outmatched by the Centauri and G'Kar begs for involvement by the League of Non-Aligned Worlds. None of the member nations can offer direct support and G'Kar feels he and his world are being abandoned. Lt. Commander Ivanova is assigned the task of introducing a newly contacted race, the Lumati, to Babylon 5 in the hopes of forming an alliance with them. She is asked to finalize the alliance in a very personal way. Due to his ties with Mr. Mordan, Londo's rise as a power to be reckoned with has left him feared and alone. Security officer Zack Allan joins the team at Babylon 5.

Episode 35:  "Hunter, Prey"

Dr. Everett Jacobs, personal physician to the president, is on the run, pursued by Earth Special Intelligence to Babylon 5. Dr. Everett has accessed classified information that Earth Force is willing to suppress at any cost, information that implicates President Clark in the death of his predecessor President Santiago. While Earth Force directs Sheridan to help find Dr. Jacobs, he is secretly trying to help him escape. Commander Sheridan makes it his personal mission to get to know Kosh and ends up feeling he is being toyed with.

Episode 36:  "There All the Honor Lies"

Sheridan is involved in the death of a Minbari and could be charged with murder. Delenn is instructed by her government to conduct her own investigation while at the same time Garibaldi mounts his investigation. It is during these investigations Sheridan learns that Minbari never lie, or so it is believed. Meanwhile Earth Dome assigns Sheridan a lawyer who informs him he is to be indicted on murder charges and that the charges alone could result in his removal as Commander of Babylon 5. In the middle of all this, Kosh insists on spending time with Sheridan, the first in a series of lessons on how to fight legends.

Episode 37:  "And Now For a Word"

Interstellar News (ISN) spends 36 hours on Babylon 5 for an in-depth report. This entire episode is seen from the perspective of the news reporters. During their visit the Narn and Centauri conflict spills over into B5 territory. G'Kar insists that Earth take a stand on the conflict one way or another. The Narns and the Centauri take matters into their own hands and begin open fighting outside the station. Sheridan has no choice now but to get involved and fires on the battling ships outside the station. Two Centauri transports are captured and brought into the station for inspection. The Centauri object and send a heavy battle cruiser to blockade B5 until the ships are returned. This prompts the Narns to send their own battle cruiser and before long the two warships destroy each other. As ISN prepares to depart B5 they ask members of the command staff if Babylon 5 is serving its intended purpose as a place of peace and whether or not it is all worth it.

Episode 38:  "In The Shadow of Z'ha'dum"

We learn that Captain Sheridan's wife Anna was a scientist aboard the science vessel Icarus, reported destroyed with no survivors while exploring a dead world on the rim of the galaxy. While going through some of her belongings he learns there is a survivor from the Icarus who has been visiting Babylon 5, the mysterious Mr. Mordan. Sheridan has him detained without cause and demands answers even if it means losing his command. Delenn and Kosh warn Sheridan that if Mr. Mordan is not released all will be lost. Sheridan learns for the first time of the existence of the "Shadows", an ancient enemy billions of years old who has returned, and that Mr. Mordan is connected to them. The newly formed Ministry of Peace visits Babylon 5 and enlists recruits into the Nightwatch, an organization created to serve the interest of peace by encouraging its members to spy on those who sow the seeds of dissent.

Episode 39:  "Knives"

Garibaldi tells Sheridan about the Babylon 5 "triangle". A section of the station where unexplained things happen. Sheridan is intrigued and decides to visit the section himself. He comes upon the body of an apparently dead alien that attacks him and transfers some kind of life form to him. Following this incident, Sheridan begins hallucinating, the result of the life form within Sheridan attempting to communicate with him through shared memories. Sheridan finds himself driven to return to sector 14, the site of the time distortion field were Babylon 4 disappeared. Londo gets a visit from a childhood friend who needs his help. He is being targeted by the changing powers that be at Centauri Prime and is concerned for the safety of his family. The only way he can save face and protect his family name is by challenging Londo to a duel to the death and letting Londo kill him.

Episode 40:  "Confessions and Lamentations"

The Markab aboard the station are dying at an unusually fast rate and they object to Dr. Franklin investigating into the matter. Dr. Franklin discovers the entire Markab race is dying of an infectious disease that threatens all on Babylon 5. Sheridan orders a station wide quarantine and halts all traffic to and from Babylon 5. Dr. Franklin further learns that the Markab leadership regards the deadly disease as an unclean disease spread by the immoral among their race and see the disease as punishment for an impure and immoral life style. As a result the Markab never dealt with the disease openly and honestly and now it is too late.

Episode 41:  "Divided Loyalties"

Lyta Alexander returns to Babylon 5 injured and unconscious aboard a damaged transport. While on Mars she learned of a secret Psi Corp program to produce sleeper agents who are unaware themselves they are spies. She informs the command staff they have a sleeper agent among them and that she can identify the agent if allowed to transmit a trigger telepathically to each one of them. After an attempt is made on her life Sheridan agrees to allow the telepathic trigger to be tested on each member of his command staff. Lt. Commander Ivanova objects to the procedure as a personal invasion and confesses to Sheridan she is a latent telepath. Each member of the command staff is subjected to the telepathic trigger and the sleeper agent is finally identified.

Episode 42:  "The Long, Twilight Struggle"

Londo Mollari returns to Centauri Prime and is informed by Lord Refa of plans to end the war with the Narns. Londo is to play a key role and must once again ask for a favor from Mr. Mordan. The Narns are losing the war and so plan an aggressive attack against a Centauri supply post that will require the bulk of the Narn fleet leaving their home world with only a skeleton defense. Lord Refa learns of the Narns plan and intends to commit the Centauri fleet to Narn if Londo can commit his forces to the supply post. Arriving at Narn with the Centauri fleet, Lord Refa uses mass drivers to flatten Narn, sending it back to the stone age. Narn has no choice but to surrender. Draal, the guardian of the great machine on Epsilon 3, appears to Sheridan and Delenn and bids them to pay him a visit in person. Delenn decides it is time to introduce Sheridan to the Rangers and transfers equal authority over the Rangers to Sheridan.

Episode 43:  "Comes the Inquisitor"

Kosh calls for Delenn and tells her an Inquisitor is coming and that she is to submit to his authority. The Vorlons want to put Delenn through a test to make sure she is the right person in the right place at the right time for the coming darkness that is before them. The Inquisitor turns out to be an infamous figure right out of Earth's history, taken by the Vorlons hundreds of years ago and kept alive until needed. The Inquisitor asks Delenn questions and with each inadequate answer inflicts pain on her. The interrogation escalates into torture and Sheridan intervenes and so the Inquisitor takes Sheridan in her place. The Narns begin to question G'Kar's leadership and gives him a task to perform to prove his abilities.

Episode 44:  "The Fall of Night"

Now that the Narn-Centauri War is over the Centauri are invading neighboring territories, threatening to destabilize the entire area. A VIP from the Ministry of Peace arrives on Babylon 5 with the intention of forming an alliance with the Centauri and signing a non-aggression treaty with them. Meanwhile, a lone surviving Narn heavy cruiser arrives at Babylon 5 in need of repair and requests sanctuary. Sheridan grants them sanctuary and orders his people to keep the presence of the Narn ship behind Epsilon 3 a secret. The information is leaked, due to Nightwatch members, and the Centauri send a battle cruiser to intercept. Unable to control the Centauri, they fire on both the Narn ship and Babylon 5. Sheridan is forced to destroy the Centauri cruiser. Following this incident Sheridan is ordered to give the Centauri a formal apology. While on his way to address the ambassadors, Centauri agents attempt to kill Sheridan, blowing up the station's shuttle he his riding. Sheridan jumps free at the last moment but is heading toward the station's floor to his death. The only one who can save Sheridan is Kosh now and he finally reveals himself. A star fury pilot is killed by a Shadow vessel in hyperspace but not before the pilot records images of the vessel and ejects the recording.