'Counterpart': 4 Big Burning Questions for Season 2

THR takes a deep dive into the dangling threads after Sunday's season-one finale.
Nicole Wilder/Starz

The Starz spy-fi series Counterpart ended its critically praised first season Sunday with more questions than answers. In a climactic moment, Howard Silk (J.K. Simmons) — a secret agent from our Earth — killed Alexander Pope (Stephen Rea), the mysterious leader of Project Indigo, an organization bent on revenge for the deadly flu pandemic that decimated his alternate Earth 20 years before, killing more than half a billion people.

Silk was captured by Ian Shaw (Nicholas Pinnock), an aggressive agent from the Department of Housekeeping for the Office of Interchange (aka the spy agency in charge of hiding and regulating the crossing between the two Earths.

Every person on our Earth has a doppelganger on the other side: the people on our side are designated “Alpha,” while the doubles on the other side are referred to as “Prime.” Given the byzantine spy plots, it was expected to have a number of dangling threads waiting to be tied up in future episodes. Here are the four biggest questions remaining heading into the previously announced second season of the Starz drama.

Where is Howard Alpha Being Held Captive?

Ian, who has had an ongoing romantic relationship with fellow spy Emily Prime (Howard’s ex-wife, played by Olivia Williams), takes custody of Howard Alpha after the Pope killing and demands to never see him again. Howard is taken, cuffed and put into a small windowless room with only a folding chair inside. Is this an OI black site? Ian’s motivation to isolate Howard is one of pure jealousy, since witnessing the burgeoning romance between Howard Alpha and Emily Prime. Logic would dictate that Howard can only be held for so long without being released, so this should be resolved fairly quickly. The dramatic triangle, however, will only intensify.

What Happens When Emily Alpha Wakes Up From Her Coma?

On our Earth, Howard Prime is trapped due to the fallout from the Indigo terrorist attack on the crossing between universes at the OI Headquarters. Emily Alpha, who is still married to Howard on this side, has been in a coma since Alexander Pope engineered an attack on her. Howard Prime has developed romantic feelings for her, even though she isn’t really his wife, and has taken it upon himself to protect her at all costs. Emily Alpha is also a spy and has been used as a contact by Howard Prime for years. Emily Prime woke up briefly at the end of season one but has not shown any signs of actual consciousness. When she finally wakes up, how will she react to the fact that her husband is trapped on the other side, and that the man in front of her has fallen for her while she’s been asleep? Very little is known about her, but it was revealed that Emily had an affair with another man previously, so she may be more like Emily Prime than Howard is counting on.

What Will Happen to Project Indigo Now That Alexander Pope is Dead?

Throughout the season it has been definitively shown that Alexander Pope was the mastermind of Project Indigo. The mission of Indigo is to take children, indoctrinate them, train them to be sleeper agents and take over the lives of their doubles on our Earth. Clare (Nazanin Boniadi) was the first agent sent, who killed and took over the life of the wife of Peter Quayle (Harry Lloyd), a highly placed officer in the OI. She later engineered the attack on the OI Headquarters.

The children are trained at an Indigo “school,” where they are taught every aspect of their doppelgangers’ lives, waiting patiently for a future insertion. Mira (Christiane Paul) is the head of the school, having taught Clare and numerous others. In episode eight, Ian’s team raids the school. The children all take cyanide pills, committing suicide to avoid capture. Mira barely escapes, so it is a good guess that she may fill the power vacuum left by the killing of Alexander Pope.

Who Is Responsible for the Flu Pandemic?

Our Earth vehemently denies releasing the pandemic on the alternate universe, but Alexander Pope started Project Indigo as a way to get revenge based on his perception that our Earth wants to destroy the people of the parallel one in order to take the planet’s resources and use them for their own gain. Pope could have released the virus himself, however, to drum up support for an attack on our Earth. Since Pope is now dead, it may, in fact, be “management,” the unseen power brokers of the OI who are responsible for the release. The jury is still out on whether the flu pandemic was accidental or a deliberate act of destruction. Given the nature of the show, an act of war is much more likely.

What are your theories for Counterpart season two? Sound off in the comments section.