It seems that perhaps the Andromeda writers like to write their episodes in trilogies. These are the ones I have found so far in the first two seasons.

Restorian
D Minus Zero- the mysterious attacker.
The Ties That Blind- The attacker revealed as the Restorians.
Star-Crossed- the leader behind the Restorians revealed.

Magog Leader
Harper 2.0- The introduction of the Magog leader.
Its Hour Come At Last- The Magog world ship.
The Widening Gyre- The coming Magog invasion.

The Progenitor Saga
Double Helix- Introduction of the Tyr's connection to the Progenitor.
Music of a Distant Drum- Tyr steals the Progenitor's body.
Exit Strategies- Tyr faces off with his allies who helped him steal the body.

Possible Triliogy
Mad Persied/Search for Tarn Vedra story line

Fear & Loathing in the Milky Way Galaxy- The Mad Persied's diary is found.
It Makes A Lovely Light- botched attempt to make it to Tarn Vedra.

Possibly any future episodes dealing with the above mentioned will be trilogies as well.

Looks like the Progentior saga has another entry.
Una Salus Victus in which the Kazov try to reclaim the body. This could be considered the start of another trilogy.