- "A show of force is required. If they know we're here, they'll be less likely to start something."
- – Captain Pierce
In 2258, while en route to the Vega Colony, Pierce received orders via the Office of Planetary Security to take his ship directly to Babylon 5 and assume control. The station commander, Jeffrey Sinclair, had just discovered the Great Machine on Epsilon III. Faced with overwhelming potential for technological discoveries, Earthforce wanted the Hyperion at the station to stake a claim for the Earth Alliance.
Upon his arrival, Pierce met with Sinclair and explained the situation. Sinclair immediately rebuked Pierce, telling him that the station was no place for Earthforce "saber rattling." Angered over Sinclair's reaction, Pierce decided to send a team to Epsilon III on his own. As his ships tried to get past the planet's defense systems, he was told by Sinclair that they need a jamming device, which is being repaired on the station.
Pierce eventually realized Sinclair was lying about such a device so he decided to send another team, despite the warnings of Varn, an alien brought back from the planet. Varn had told Sinclair that if anyone goes to the surface, the Great Machine will self-destruct, blowing up the entire planet. Pierce was surprised when Sinclair ordered to activate Babylon 5's defense grid, promising to open fire on Pierce's ships if they tried to land. Pierce reluctantly recalled his ships, but, soon, a strange alien vessel jumped into local space and laid a claim to the Great Machine. Pierce immediately denied the claim and ordered the aliens to withdraw.
Pierce contacted Sinclair again, saying they must coordinate to fight the alien and he believed they could repel it together. Sinclair reluctantly agreed, and Pierce was right, as Varn was taken onto a ship headed for the planet. Angered, the alien ship attacked. Babylon 5 and the Hyperion coordinated a counterattack, but they were nearly overwhelmed. Fortunately, Draal took over at the heart of the Great Machine and intervened. He issued an edict forbidding anyone to approach the planet, and, when the alien ship defied him, he destroyed it.